Abstract
Bacteriophages of freshwater environments have not been well studied despite their numerical dominance and ecological importance. Currently, very few phages have been isolated for many abundant freshwater bacterial groups, especially for the family Comamonadaceae that is found ubiquitously in freshwater habitats. In this study, we report two novel phages, P26059A and P26059B, that were isolated from Lake Soyang in South Korea, and lytically infected bacterial strain IMCC26059, a member of the family Comamonadaceae. Morphological observations revealed that phages P26059A and P26059B belonged to the family Siphoviridae and Podoviridae, respectively. Of 12 bacterial strains tested, the two phages infected strain IMCC26059 only, showing a very narrow host range. The genomes of the two phages were different in length and highly distinct from each other with little sequence similarity. A comparison of the phage genome sequences and freshwater viral metagenomes showed that the phage populations represented by P26059A and P26059B exist in the environment with different distribution patterns. Presence of the phages in Lake Soyang and Lake Michigan also indicated a consistent lytic infection of the Comamonadaceae bacterium, which might control the population size of this bacterial group. Taken together, although the two phages shared a host strain, they showed completely distinctive characteristics from each other in morphological, genomic, and ecological analyses. Considering the abundance of the family Comamonadaceae in freshwater habitats and the rarity of phage isolates infecting this family, the two phages and their genomes in this study would be valuable resources for freshwater virus research.
Highlights
Bacteriophages are the smallest but the most abundant biological entities on earth[1]
In a similarity analysis of the 16 S rRNA gene sequences using EzBioCloud[28], IMCC26059 showed a close relationship with several type strains of the family Comamonadaceae: Curvibacter delicatus (97.93%), Curvibacter fontanus (97.92%), Rhodoferax saidenbachensis (97.85%), and Albidiferax ferrireducens (97.27%)
A phylogenetic tree built based on 16 S rRNA gene sequences placed IMCC26059 clearly within the family Comamonadaceae, the taxonomic status within the family could not be resolved unambiguously (Supplementary Fig. S1)
Summary
Bacteriophages (phages) are the smallest but the most abundant biological entities on earth[1]. Without the need of culturing both bacteria and phages, virome analysis provided access to large amounts of bacteriophage genomes in the environment. Many studies reported novel and abundant bacteriophage genomic contigs in various environments[7,8,9]. The phages infecting the LD28 bacterial clade were cultured from an oligotrophic freshwater lake[17], and metagenome-assembled genomes of the phages that are considered to infect the acI clade were retrieved from viromes[18]. To obtain more freshwater phages that infect Comamonadaceae, lytic bacteriophages have been screened from Lake Soyang using the IMCC26059 strain as a host, which resulted in the successful isolation of two phages, P26059A and P26059B. The distribution of the two phages in diverse freshwater environments was determined using the genomes of the phages and freshwater virome data, contributing to the understanding of freshwater phage populations and their diverse genomes
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