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

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.

Keywords: Candidate phyla radiation; Complete genomes; Metagenomics; Peregrinibacteria; Strain variation.

Figure 1. Phylogenetic placement of the Ca. P. riflensis genomes.

(A) 16S rRNA and (B) concatenated ribosomal protein trees showing the phylogenetic placement of the Ca. P. riflensis genomes inferred by maximum likelihood. Bootstrap values (percent of 1000 bootstrap repetitions) are marked on internal nodes. Only bootstrap values ≥50 are shown.

Figure 2. Diagram showing the form of variation that distinguishes the five closely related genomes.

Coding Region on the genome is shown in yellow. Colors on the identity bar reflect similarity between the five genomes: Green, 100%; Olive, 80%; Red, 40%; Black, 20%.

Figure 3. Overview of the protein investments in biosynthesis in Ca. P. riflensis.

TCA, Tricarboxylic acid cycle; NADPHX, Reduced nicotinamide adenine dinucleotide phosphate; FMN, Flavin mononucleotide; FAD, flavin adenine dinucleotide; PEP, phosphoenolpyruvate; THF, Tetrahydrofolic acid; PPi, Pyrophosphate; PFOR, pyruvate:ferredoxin oxidoreductase.

Figure 4. Plot of GC skew over the Ca. P. riflensis str.RIFOXYC2_FULL_PER-ii_58_32 genome.

(A) Plot of GC skew indicating the locations of the origin/terminus of replication. The plot has the expected form, providing added confidence about the accuracy of the assembly. (B) Localization of short repeats in the identified origin of replication. E. Coli DNaA box sequences are shown for reference.