Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum.

Karthik Anantharaman,Alexander J Probst,Kenneth H Williams,Cindy J Castelle,Brian C Thomas,Jillian F Banfield,Christopher T Brown,David Burstein

doi:10.7717/peerj.1607

Abstract

Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.

Highlights

Metagenomic analyses of microbial communities in natural environments have revealed numerous previously unrecognized microorganisms, including those described to beHow to cite this article Anantharaman et al (2016), Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum
The average length of the complete genomes was 1,248,071 ± 217 bp, a result that confirms the previous prediction of small genome size that was made based on genome completeness estimates and draft genome lengths (Wrighton et al, 2012)
The sequences from the genomes reported here, those of GWC2_PER_54_8 and a highly similar genotype GWB1_PER_54_8, and clone sequences identified in the SILVA database (Pruesse et al, 2007), branch separately from the other Peregrinibacteria for which partial genomes are available

Summary

Introduction

Metagenomic analyses of microbial communities in natural environments have revealed numerous previously unrecognized microorganisms, including those described to beHow to cite this article Anantharaman et al (2016), Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. The Reference sequence database comprised proteins from 11 previously identified Peregrinibacteria, and Berkelbacteria (Wrighton et al, 2012; Brown et al, 2015) that served as an outgroup. No insertion sequences, such as reported in many CPR bacteria, were identified in the 16S rRNA genes (Brown et al, 2015).

Results

Conclusion