Isolation and Characterization of the First Freshwater Cyanophage InfectingPseudanabaena

Abstract

Cyanobacteria are the major primary producers in both freshwater and marine environments. However, the majority of freshwater cyanophages remain unknown due to the limited number of cyanophage isolates. In this study, we present a novel lytic freshwater cyanophage PA-SR01 which was isolated from Singapore Serangoon Reservoir. To our knowledge, this is the first isolate of cyanophage that has been found to infect the cyanobacterium Pseudanabaena. PA-SR01 has a narrow host range, a short latent period and is chloroform sensitive. Distinct from the majority of cyanophage isolates, PA-SR01 has a tail-less morphology. It is a double-stranded DNA virus with a 137,012 bp genome. Functional annotation for the predicted open reading frames (ORFs) of PA-SR01 genome identified genes with putative function related to DNA metabolism, structural protein, lysis, host-derived metabolic genes and DNA packaging. Out of 166 predicted ORFs, only 17 ORFs have homology with genes with known function. Phylogenetic analysis of the major capsid protein and terminase large subunit further suggests that Phage PA-SR01 is evolutionary distinct from known cyanophages. Metagenomics sequence recruitment onto PA-SR01 genome indicates that PA-SR01 represents a new evolutionary lineage of phage which shares considerable genetic similarities with phage sequences in aquatic environments and could play key ecological roles. IMPORTANCE This study presents the isolation of the very first freshwater cyanophage PA-SR01 infecting Pseudanabaena and fills important knowledge gap on freshwater cyanophage as well as cyanophages infecting Pseudanabaena.

Novel Freshwater Cyanophages Provide New Insights into Evolutionary Relationships between Freshwater and Marine Cyanophages

“…This finding is also reflected in the genes shared between S-SRP01 and marine cyanopodovirus isolated from estuaries of Chesapeake Bay. As seen in Table S4, approximately 20% ( 13 ) of S-SRP01 ORFs share best-hit with protein sequences from S-CBP3 and S-CBP4. Similarly, significant gene sharing was observed in the S-SRM01 genome with cyanomyoviruses, such as P-SSM2 (19 ORFs with best-hit) and S-PM2 (9 ORFs with best-hit) (Table S5).…”

“…Terminase large subunit ( Terl ) genes have been used widely for comparing cyanophage phylogenies in various studies ( 13 , 20 , 30 , 42 ). DNA polymerase genes and major capsid genes were also used as marker genes in many studies to compare the cyanophage community ( 43 , 44 ).…”

“…Cyanophage amplification and purification were carried out as described previously ( 13 ). Briefly, 1% (vol/vol) of the virus isolate was added to 30-ml cultures of host cyanobacteria to produce enough phage progeny for the subsequent analysis.…”

Genomic Characterization of a Novel Freshwater Cyanophage Reveals a New Lineage of Cyanopodovirus

“…The Synechococcus sp. strain SR-C1 was isolated as described previously (Zhang et al, 2020). The strains were isolated by micro-pipetting from a freshwater lake sample into sterile MLA medium (Bolch and Blackburn, 1996) at 25 • C. Identification of the strains was determined through whole genome sequencing (Gin et al, 2021).…”

Viruses of freshwater bloom‐forming cyanobacteria: genomic features, infection strategies and coexistence with the host

“…Thus, low initial abundances of both cyanobacteria and cyanoviruses prevent cyanovirus ability to control cyanobacteria population dynamics at the exponential phase. Finally, relatively low rate (20%-30%) and long-time (hours to tens of hours) of adsorption to the host cell surface, relatively long latent period (hours to days) and high rate of infectivity loss (minutes-hours) outside the cell, properties which were attributed to most of the isolated cyanoviruses infecting various freshwater bloom-forming cyanobacteria (Gao et al, 2009;Liao et al, 2010;Šulčius et al, 2015;Coloma et al, 2017;Zhang et al, 2020), would further limit their interactions with cyanobacteria at the bloom onset. Thus, one could expect that the effect of cyanoviral infection and lysis is relatively negligible during the exponential phase of the bloom.…”