Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages

Abstract

Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.

Keywords: Pbunaviruses; Pseudomonas phage PB1; bacteriophage; uncultivated phage genomes.

Figure 1

Phylogenetic comparison of PCR amplicons of the genes encoding hypothetical proteins PB1_gp84, 85, 86 generated from environmental DNA. Neighbor-joining tree was generated based on the Jukes-Cantor distance method.

Figure 2

PB1 genome atlas, demonstrating quality hits to the PB1 genome across environmental viral metagenomes. Genes for which no hit was detected are indicated by grey. The bar graph at the top of the figure represents amount of data collected for that sample.

Figure 3

(a) Genome map of PB1-like genomes. CDS regions which are missing/disrupted in the new uncultivated viral genomes are indicated (A = All 9 genomes; G = Gallinipper; J = Jollyroger; K = Kraken; L = Kula; M = Nemo; N = Nessie; P = Poseidon; S = Smee; T = Triton). (b) Phylogenetic comparison of uncultivated Lake Michigan PB1-like viruses (red) to Pseudomonas-infecting Pbunaviruses. PB1 strains indicated in blue font are phages previously cultured and isolated from Lake Michigan [50].