Abstract
Numerous studies have revealed the high diversity of cyanophages in marine and freshwater environments, but little is currently known about the diversity of cyanophages in paddy fields, particularly in Northeast (NE) China. To elucidate the genetic diversity of cyanophages in paddy floodwaters in NE China, viral capsid assembly protein gene (g20) sequences from five floodwater samples were amplified with the primers CPS1 and CPS8. Denaturing gradient gel electrophoresis (DGGE) was applied to distinguish different g20 clones. In total, 54 clones differing in g20 nucleotide sequences were obtained in this study. Phylogenetic analysis showed that the distribution of g20 sequences in this study was different from that in Japanese paddy fields, and all the sequences were grouped into Clusters α, β, γ and ε. Within Clusters α and β, three new small clusters (PFW-VII∼-IX) were identified. UniFrac analysis of g20 clone assemblages demonstrated that the community compositions of cyanophage varied among marine, lake and paddy field environments. In paddy floodwater, community compositions of cyanophage were also different between NE China and Japan.
Highlights
Viruses are recognized as the most abundant biological entities on earth [1,2]
After analyzing all of the clone positions of an individual sample in Denaturing gradient gel electrophoresis (DGGE) gel and deleting clones with identical nucleotide sequences, 54 clones with different g20 sequences were obtained in this study
Green triangles and blue circles indicate g20 clones obtained from lake freshwater and marine water, respectively; Black and white square boxes indicate g20 clones obtained from paddy field soils in Japan and paddy floodwaters in Japan, respectively; White triangles indicate g20 clones obtained from paddy floodwaters in NE China
Summary
Viruses are recognized as the most abundant biological entities on earth [1,2]. As mortality agents affecting heterotrophic and photosynthetic microbes, viruses play important roles in regulating the microbial population and community structure [3], mediating gene transfer between microorganisms [4,5], and driving the global biogeochemical nutrient cycle [4,5]. Bacteriophages (phages) represent the majority of viruses in the natural environments [1,2]. Cyanophages are viruses that are able to infect cyanobacteria. Unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant forms of marine picoplankton [9,10], whereas filamentous cyanobacteria such as Nostoc, Anabaena, Cylindrospermum, and Phormidium are dominant forms in freshwater [11]. Several cyanophages that infect filamentous cyanobacteria have been isolated from freshwater with solid or liquid medium, research on their genetic diversity is limited [12,13]. The knowledge of the genetic diversity of cyanophages is mainly based on the phages infecting oceanic Synechococcus and Prochlorococcus [14,15,16]. Most cyanophages are classified into the three-tailed phage families Myoviridae, Podoviridae, and Siphoviridae, among which cyanomyoviruses represent more than 80% of cyanophage isolated from the marine environments [6,14]
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