Isolation and genome analysis of a novel Synechococcus cyanophage Yong-L2-223

Abstract:

[Objective] Cyanophages, the viruses specifically infecting cyanobacteria, are ubiquitous in water environments. They play a role in regulating the population dynamics and density of cyanobacteria and promote the biogeochemical cycling of the aquatic ecosystem. This study aims to isolate and identify a cyanophage. [Methods] A novel cyanophage Yong-L2-223 was isolated from fresh water samples with marine Synechococcus sp. PCC 7002 as the indicator host. The host range, genome sequence, open reading frames (ORFs), and phylogenetic relationship of Yong-L2-223 were studied. [Results] The host range tests against 31 strains of cyanobacteria showed that Yong-L2-223 could infect the indicator host PCC 7002 (Synechococcales) and two freshwater strains Microcystis viridis FACHB-1342 (Chroococcales) and Aphanizomenon flos-aquae FACHB-1209 (Nostocales) from the Dianchi Lake. The infection of the cyanobacterial strains from both the seawater and freshwater samples indicated that Yong-L2-223 was a euryhaline cyanophage. Yong-L2-223 was myovirus-like, consisting of an icosahedral head (about 60 nm in diameter) and a contractile tail (about 136 nm in length). The genome (double-stranded DNA) of Yong-L2-223 had a length of 65 725 bp, with the G+C content of 58.6% and 100 ORFs. It was predicted to carry the Cas4 gene, gene transfer factor (GTA) gene, auxiliary metabolic genes (AMGs), and a gene cluster for the synthesis of pre-Q0. These genes may contribute to the adaptation and infection of the cyanophage in cyanobacteria of three orders. The pairwise sequence comparison (PASC) illustrated that the highest similarity sharing by cyanophage Yong-L2-223 and all the viruses in the current genome databases was only 3.78%, far below the genus boundary cut-off of 70% defined by the International Committee on Taxonomy of Viruses. In the phylogenetic tree based on the whole proteomes, Yong-L2-223 formed an independent branch, with long evolutionary distances from other phages. [Conclusion] Yong-L2-223 is a new genus of the Caudoviricetes class. For the first time, we used a marine cyanobacterial strain as the indicator host to isolate and obtain a novel cyanophage from freshwater, which broadened the understanding of cyanophages, enriched cyanophage genome database, and laid a foundation for the development of cyanophage resources.