Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

Abstract

The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.

Expansion of Known Rhodobacter capsulatus Bacteriophage Diversity with 24 Additional Genomes

“… Rhodobacter capsulatus , a freshwater alphaproteobacterium, was the first microorganism found to perform horizontal gene transfer with a bacteriophage-like gene transfer agent (RcGTA) ( 1 ). Recent studies found that many bacteriophages that infect this host share genes with RcGTA ( 2 – 6 ). Prior to this announcement, 29 R. capsulatus phage genomes were organized into six distinct clusters (RcA to RcF), with four remaining as singletons ( 2 ).…”

“…Recent studies found that many bacteriophages that infect this host share genes with RcGTA ( 2 – 6 ). Prior to this announcement, 29 R. capsulatus phage genomes were organized into six distinct clusters (RcA to RcF), with four remaining as singletons ( 2 ). To advance our understanding of these phages and RcGTA, we have expanded this collection with 24 genomes from isolates collected throughout the state of Illinois.…”

“…Phages were discovered using previously described enrichment protocols, where 10-mL environmentally collected water samples were combined with 10 mL of fresh yeast extract-peptone medium and 10 mL of R. capsulatus strain YW1 culture grown to an optical density at 600 nm (OD 600 ) of ~1.0 ( 2 ). After 3 to 5 of days shaking at 30°C, samples were filtered through 0.22-μm filters and plated with a 0.4% top agar overlay embedded with R. capsulatus cells.…”