Rapid Microcystis Cyanophage Gene Diversification Revealed by Long- and Short-Term Genetic Analyses of the Tail Sheath Gene in a Natural Pond

Abstract

Viruses influence the abundance of host populations through virus-mediated host cell lysis. Viruses contribute to the generation and maintenance of host diversity, which also results in viral diversity throughout their coevolution. Here, to determine the phage gene diversification throughout the coevolution of host and phage in a natural environment, we investigated the genetic diversity and temporal changes in Microcystis cyanophage populations using a total of 810 sequences of the Ma-LMM01-type cyanophage tail sheath gene (g91) from 2006 to 2011 in a natural pond. The sequences obtained were highly diverse and assigned to 419 different genotypes (GT1 to GT419) clustered at 100% nucleotide sequence similarity. A maximum-parsimony network showed that the genotypes were largely divided into three sequence groups, which were dominated by major genotypes (more than 24 sequences: GT2, GT53, and GT163 in group I; GT25 in group II; and GT1 in group III). These major genotypes coexisted and oscillated throughout the sampling periods, suggesting that the Microcystis-cyanophage coevolution was partly driven by a negative frequency-dependent selection. Meanwhile, the high viral genetic diversity observed was derived from a large number of the variants of each major and moderately frequent genotype (including 7 to 18 sequences: GT7, GT26, GT56, GT149, and GT182 in group I; GT152 in group II) (1 or 2 nucleotide substitutions). The variants almost always co-occurred with their origin genotypes. This manner of variant emergence suggests that increased contact frequency within a host-phage population promotes rapid coevolution in a form of "arms race."

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…Our level of knowledge regarding the total diversity and genetic composition of environmental phages is minimal. Evidence suggests that communities of phages found in freshwaters are likely to represent a more complex cohort than that of their marine counterparts (Kimura et al 2013;Baker et al 2006), in congruence with the more heterogeneous nature of freshwater. Broadly speaking, in comparison to marine communities, freshwaters are understudied regardless, and so the scope of this expected greater diversity is unknown.…”

Cyanophages Infection of Microcystis Bloom in Lowland Dam Reservoir of Sulejów, Poland

“…1). The mcy gene cluster and mechanism of production of the microcystin molecule may not affect the metabolic pathway or the mechanism of phage replication inside the host cell, which, as suggested by Kimura et al [33], depends mostly on the photosynthetic system of cyanobacteria.…”

“…This could prevent the detection of subtle changes between phage genotypes occurring as a result of point mutations. In a study of Kimura et al [33], the analysis of phylogenetic affiliations based on a longer fragment of the g91 gene (approximately 500 bp) enabled diversification and identification of more than 400 phage genotypes. Therefore, the diversity of Microcystis specific phages in the context of long-term monitoring of the Sulejów Reservoir will be assessed in future studies using larger fragments of the g91 gene, as suggested by Kimura et al [33].…”

“…Five of these studies focused on the dynamics of occurrence of phages specific to the Microcystis genus [12,13,19,20,33], and one study examined cyanophage gene diversification [35]. However, these studies were limited to regions of East Asia (Lake Mikata, Japan; Hirosawanoike Pond, Japan; and East Lake, China), and water factors that may influence viral infection were not identified.…”

“…Molecular genomic analysis of this strain led to the identification of the g91 gene, which was characterized as a viral sheath protein-encoding gene [12,13,19,26,33,34].…”