Nearly Identical Bacteriophage Structural Gene Sequences Are Widely Distributed in both Marine and Freshwater Environments

Abstract

Primers were designed to amplify a 592-bp region within a conserved structural gene (g20) found in some cyanophages. The goal was to use this gene as a proxy to infer genetic richness in natural cyanophage communities and to determine if sequences were more similar in similar environments. Gene products were amplified from samples from the Gulf of Mexico, the Arctic, Southern, and Northeast and Southeast Pacific Oceans, an Arctic cyanobacterial mat, a catfish production pond, lakes in Canada and Germany, and a depth of ca. 3,246 m in the Chuckchi Sea. Amplicons were separated by denaturing gradient gel electrophoresis, and selected bands were sequenced. Phylogenetic analysis revealed four previously unknown groups of g20 clusters, two of which were entirely found in freshwater. Also, sequences with >99% identities were recovered from environments that differed greatly in temperature and salinity. For example, nearly identical sequences were recovered from the Gulf of Mexico, the Southern Pacific Ocean, an Arctic freshwater cyanobacterial mat, and Lake Constance, Germany. These results imply that closely related hosts and the viruses infecting them are distributed widely across environments or that horizontal gene exchange occurs among phage communities from very different environments. Moreover, the amplification of g20 products from deep in the cyanobacterium-sparse Chuckchi Sea suggests that this primer set targets bacteriophages other than those infecting cyanobacteria.Unicellular cyanobacteria are a major component of the prokaryotic biomass in the oceans (6, 15), account for more than half of the fixed carbon in some regions, and play a key role in the transfer of energy through the microbial loop (6,15,21). Consequently, knowledge of the regulation of cyanobacterial communities is required to understand global nutrient and energy cycles.Viruses are the most abundant biological entities in fresh and marine waters and are typically 5-to 10-fold more abundant than prokaryotes (1,19,29). As mortality agents of heterotrophic and photosynthetic microbes (8,25,37), they affect the abundance and diversity of host cell communities (13, 18) as well as the cycling of carbon and nutrients (37).The proportion of primary producers lost to viral lysis is uncertain; however, viruses infecting a single strain of the marine cyanobacterium Synechococcus are widespread and can reach levels of abundance of Ͼ10 5 ml Ϫ1 (16,27,36). Estimates from the proportions of visibly infected cells and viral decay rates suggest that approximately 3 to 10% of Synechococcus spp. are destroyed daily by viral lysis (19,26,37).The impact of viruses on host communities can be inferred from viral community diversity, as viral taxonomy can provide insights into the hosts that they infect. For example, phylogenetic analyses of algal virus DNA polymerase genes revealed that phycoviruses are monophyletic relative to other viral families and that genetically distinct groups are clearly resolved and correspond to the host taxon infected (3, 4). Subsequ...

Previously unknown and highly divergent ssDNA viruses populate the oceans

“…This is consistent with some groups of viruses being widely distributed in nature (Short and Suttle, 2002;Breitbart and Rohwer, 2005;Short and Suttle, 2005;Labonté et al, 2009), while others are more restricted in distribution (Short and Suttle, 2005;Tucker et al, 2011).…”

Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses

“…Such characteristics allow local dynamics to have a dominant role in structuring microbial metacommunities and reduce the likelihood that dispersal limitation will influence spatial patterns of microbial diversity (Van der Gucht et al, 2007;De Bie et al, 2012). These predictions are consistent with the wide distribution patterns of many microbial taxa (Short and Suttle, 2002;Fenchel and Finlay, 2004;Short and Suttle, 2005) and strong associations between community composition and environmental gradients (Beisner et al, 2006;De Bie et al, 2012). However, studies covering a broad range of spatial scales, varying from widely separated extreme habitats (Papke et al, 2003;Whitaker et al, 2003), stream networks (Heino et al, 2010), rock pool clusters (Langenheder and Ragnarsson, 2007), and individual salt marshes (Martiny et al, 2011), suggest that microbial dispersal can be too slow to counteract community differentiation resulting from ecological drift.…”

The diversity of cyanomyovirus populations along a North–South Atlantic Ocean transect

“…The complexity of these processes is further confirmed by the finding that g20 is part of a region of the myoviral genome that is highly mobile and is therefore often transferred between viruses (Monod et al, 1997). Moreover, Short and Suttle (2005) have previously indicated a need for caution in attributing all g20 sequences to cyanophages. However, the improved primers used in this study (g20_CPS1.1 and g20_CPS8.1) differed from those used by Short and Suttle (2005;CPS4 and G20-2), and have been empirically tested on a wide array of cyanophage isolates (Sullivan et al, 2008).…”

“…Moreover, Short and Suttle (2005) have previously indicated a need for caution in attributing all g20 sequences to cyanophages. However, the improved primers used in this study (g20_CPS1.1 and g20_CPS8.1) differed from those used by Short and Suttle (2005;CPS4 and G20-2), and have been empirically tested on a wide array of cyanophage isolates (Sullivan et al, 2008).…”