Abstract
Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated Chaetoceros tenuissimus and C. setoensis cells. A previously unknown ssDNA virus type was detected in inoculated C. tenuissimus cells, but not in C. setoensis cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.
Highlights
Diatoms (Bacillariophyta) are unicellular, photosynthetic, eukaryotic algae found in aquatic environments worldwide
The RNA-dependent RNA polymerase (RdRp) sequences detected in C. setoensis NIES-3712 belonged to types A, B, C, D, E, F, H, O, and P (Figure 1; Table 1)
The RdRp sequences of C. tenuissimus NIES-3714 were detected in seven samples, those collected in July 2011, November 2011, July 2013, January 2014, April 2014, May 2014, and June 2014 (Table 1)
Summary
Diatoms (Bacillariophyta) are unicellular, photosynthetic, eukaryotic algae found in aquatic environments worldwide. Their contribution to global biogeochemical cycling is significant [1], and they account for approximately 40% of marine primary production [2]. Complete diatom genome sequences reported to date [3,4] have revealed many aspects of diatom evolutionary history, ecology, metabolism, and influence on biogeochemical cycling [1,5,6,7]. At least 15 different diatom viruses have been reported [9]. Recent metagenomic studies have predicted a high sequence diversity of diatom viruses in aquatic environments [11,12,13,14]
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