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

Dong Zhang,Yiliang He,Karina Yew-Hoong Gin

doi:10.3389/fmicb.2021.768868

Abstract

Cyanobacteria are one of the dominant autotrophs in tropical freshwater communities, yet phages infecting them remain poorly characterized. Here we present the characterization of cyanophage S-SRP02, isolated from a tropical freshwater lake in Singapore, which infects Synechococcus sp. Strain SR-C1 isolated from the same lake. S-SRP02 represents a new evolutionary lineage of cyanophage. Out of 47 open reading frames (ORFs), only 20 ORFs share homology with genes encoding proteins of known function. There is lack of auxiliary metabolic genes which was commonly found as core genes in marine cyanopodoviruses. S-SRP02 also harbors unique structural genes highly divergent from other cultured phages. Phylogenetic analysis and viral proteomic tree further demonstrate the divergence of S-SRP02 from other sequenced phage isolates. Nonetheless, S-SRP02 shares synteny with phage genes of uncultured phages obtained from the Mediterranean Sea deep chlorophyll maximum fosmids, indicating the ecological importance of S-SRP02 and its related viruses. This is further supported by metagenomic mapping of environmental viral metagenomic reads onto the S-SRP02 genome.

Highlights

Cyanobacteria are the dominant autotrophs in freshwater and marine environment (Agawin et al, 2003; Saad and Atia, 2014)
The reads extracted were used as query to BLASTx (E-values < 10−5, max_target_seqs = 1) against viral protein sequences containing the predicted protein sequences of S-SRP02 phage listed in Table 3 and the other 3683 phage genomes of the NCBI Reference Sequence database (RefSeq, accessed on 17th March 2021)
Infectivity of S-SRP02 was tested against local freshwater cyanobacteria isolates as well as cyanobacteria cultures obtained from overseas culture collections

Summary

INTRODUCTION

Cyanobacteria are the dominant autotrophs in freshwater and marine environment (Agawin et al, 2003; Saad and Atia, 2014). S-CRM01 was isolated from freshwater environment but shares close phylogenetic relationship with marine cyanomyoviruses (Dreher et al, 2011). This relatedness between freshwater and marine cyanophages is further supported by the isolation of S-SRM01 and S-SRP01 which shared unprecedented genetic similarity with their marine counterpart (Zhang et al, 2021). We report for the first time, the isolation and characterization of a novel freshwater cyanophage S-SRP02 infecting Synechococcus sp. Unlike the previous discovery of S-SRP01 and S-CRM01, S-SRP02 does not cluster with any established phylogenetic groups of cyanoviruses infecting Synechococcus or Prochlorococcus This phage is a distinct new member in freshwater cyanophages that infect Synechococcus, an oftendominant cyanobacterium in tropical waters. Our work on S-SRP02 expands the current understanding of freshwater cyanophage diversity and its control of potentially toxic Synechococcus populations, and highlights its ecological prevalence through identifying S-SRP02 related viruses in distant environments elsewhere

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION

DATA AVAILABILITY STATEMENT