Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences

Abstract

As a major cyanophage group, cyanobacterial podoviruses are important in regulating the biomass and population structure of picocyanobacteria in the ocean. However, little is known about their biogeography in the open ocean. This study represents the first survey of the biodiversity of cyanopodoviruses in the global oceans based on the viral encoded DNA polymerase (pol) gene. A total of 303 DNA pol sequences were amplified by PCR from 10 virus communities collected in the Atlantic and Pacific oceans and the South China Sea. At least five subclusters of cyanopodoviruses were identified in these samples, and one subcluster (subcluster VIII) was found in all sampling sites and comprised approximately 50% of total sequences. The diversity index based on the DNA pol gene sequences recovered through PCR suggests that cyanopodoviruses are less diverse in these oceanic samples than in a previously studied estuarine environment. Although diverse podoviruses were present in the global ocean, each sample was dominated by one major group of cyanopodoviruses. No clear biogeographic patterns were observed using statistical analysis. A metagenomic analysis based on the Global Ocean Sampling database indicates that other types of cyanopodovirus-like DNA pol sequences were present in the global ocean. Together, our study results suggest that cyanopodoviruses are widely distributed in the ocean but their community composition varies with local environments.

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

“…Several previous studies have examined the biogeographical distribution of specific dsDNA viruses and found that these viruses are widely distributed in nature (Kellogg et al, 1995;Suttle, 2002, 2005;Breitbart and Rohwer, 2004;Labonte et al, 2009;Huang et al, 2010). The recovery of nearly identical sequences from disparate environments throughout the world has led to the suggestion that there is a shared global gene pool for viruses (Breitbart and Rohwer, 2005;Angly et al, 2006).…”

“…The recovery of nearly identical sequences from disparate environments throughout the world has led to the suggestion that there is a shared global gene pool for viruses (Breitbart and Rohwer, 2005;Angly et al, 2006). In contrast to the cosmopolitan distribution of some dsDNA phage sequences (Breitbart and Rohwer, 2004;Short and Suttle, 2005;Huang et al, 2010), the Figure 4 Spatial variation in the diversity of the Rep gene from SARssf1 phages from different sites in the North Atlantic Ocean in 2008. Sequences were de-replicated at 99% sequence identity with gaps, then a maximum likelihood phylogeny was constructed and layered on top of a map.…”

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton

“…For example, bacteriophage structural proteins g20 (portal vertex protein) (Short and Suttle 2005;Sullivan et al, 2008) and gp23 (major capsid protein) (Filee et al, 2005;Jamindar et al, 2012) have been used to identify the diversity and distribution of cyanomyoviruses and T4-like phages. Functional genes like DNA polymerase A (Labonté et al, 2009;Huang et al, 2010) and photosystem genes psbA and psbD (Bench et al, 2007;Chenard and Suttle 2008) have been used as proxies of T7-like podoviruses and cyanophage diversity, respectively. These marker genes, which have been examined in both cultivated phages and environmental amplicon sequence data, have yielded key insights into the diversity and distribution of their respective phage targets.…”

Evidence of bacteriophage-mediated horizontal transfer of bacterial 16S rRNA genes in the viral metagenome of the marine sponge Hymeniacidon perlevis

“…Podoviridae, which have a narrow host range, are, however, less frequently isolated from seawater (Suttle, 2005;Huang et al, 2010). Sponge-derived bacteria have been shown to possess a high number of CRISPRs, indicative of the presence of phages (Webster & Taylor, 2012).…”