First evidence for the existence of pennate diatom viruses

Tomaru, Yuji; Toyoda, Kensuke; Kimura, Kei; Hata, Naotsugu; Yoshida, Mikihide; Nagasaki, Keisuke

doi:10.1038/ismej.2011.207

Cited by 43 publications

(34 citation statements)

References 13 publications

(20 reference statements)

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“…The shorter nucleic acid, therefore, may be composed of double-stranded DNA (dsDNA). A genome structure composed of covalently closed circular ssDNA that contains a partially dsDNA region has typically been observed for most ssDNA diatom viruses reported to date (12,23,28,29,30,31). Genome sequencing of CtenDNAV type II showed that the whole genome was 5,570 nt in length and that the short DNA fragment which remained after digestion with S1 nuclease was 669 nt.…”

Section: Resultsmentioning

confidence: 92%

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Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom

Kimura

Tomaru

2015

Appl Environ Microbiol

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Recent studies have suggested that diatom viruses are an important factor affecting diatom population dynamics, which in turn are important in considering marine primary productivity. The marine planktonic diatom Chaetoceros tenuissimus Meunier is a cosmopolitan species and often causes blooms off the western coast of Japan. To date, two viruses, C. tenuissimus DNA virus (CtenDNAV) type I and CtenRNAV type I, have been identified that potentially affect C. tenuissimus population dynamics in the natural environment. In this study, we successfully isolated and characterized two additional novel viruses (CtenDNAV type II and CtenRNAV type II). This paper reports the basic characteristics of these new viruses isolated from surface water or sediment from the Hiroshima Bay, Japan. The physiological and morphological characteristics of the two new viruses were similar to those of the previously isolated viruses. However, the amino acid sequences of the structural proteins of CtenDNAV type II and Cten-RNAV type II were clearly distinct from those of both type I viruses, with identity scores of 38.3% and 27.6%, respectively. Our results suggest that at least four genetically distinct viruses sharing the same diatom host are present in western Japan and affect the population dynamics of C. tenuissimus. Moreover, the result that CtenRNAV type II lysed multiple diatom species indicates that RNA viruses may affect various diatom populations in the natural environment. Following the first reports of large numbers of virus-like particles (VLP) in seawater, aquatic viruses have been intensively studied (1, 2). Despite their small size, viruses represent a large proportion of the biomass of the oceans (3) and are regarded as an important component of aquatic ecosystems; they are known to regulate carbon cycling, microbial biomass, and the genetic diversity of their host organisms (3,4,5,6). Microalgae sustain a large portion of aquatic primary production, and viruses that infect them are considered to significantly affect their population dynamics (5). To improve our understanding of aquatic ecology, microalgal viruses and their hosts should be investigated in greater detail.Marine diatoms generate as much organic carbon via photosynthesis as the globe's rainforests each year (7,8,9). Recently, several reports have suggested that diatom population dynamics are potentially affected by viruses as well as by diverse physical, chemical, and biological factors (10, 11). The cosmopolitan marine planktonic diatom Chaetoceros tenuissimus Meunier often causes blooms off the coast of western Japan. To date, two distinct viruses that infect it have been isolated and characterized: C. tenuissimus DNA virus (defined as CtenDNAV type I in this study) (12) and C. tenuissimus RNA virus (defined as CtenRNAV type I) (13). The two viruses are morphologically similar; both are icodahedral and 31 to 37 m in diameter. However, their genome structures and infectious features differ. The burst sizes (calculated on the basis of the increase in the infec...

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Section: Resultsmentioning

confidence: 92%

“…This feature corresponded to the typical genomic structure of diatom RNA viruses, including Rhizosolenia setigera RNA virus (RsetRNAV), CtenRNAV, C. socialis f. radians RNA virus (CsfrRNAV), C. sp. strain SS08-C03 RNA virus (Csp03RNAV), and Asterionellopsis glacialis RNA virus (Agla-RNAV) (13,24,25,26,31).…”

Section: Resultsmentioning

confidence: 99%

Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom

Kimura

Tomaru

2015

Appl Environ Microbiol

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“…So far, two main types of ssDNA viruses have been frequently detected in viromes: eukaryote-infecting CRESS-DNA viruses and bacteriophages from the Microviridae family. Novel and unusual ssDNA viruses continue to be isolated, particularly from eukaryotic and archaeal hosts (Tomaru et al, 2012; Mochizuki et al, 2012; Kimura & Tomaru, 2015). However, the relative abundance of ssDNA viruses among DNA viral communities remains an open and challenging question to address.…”

Section: Resultsmentioning

confidence: 99%

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

Roux

Solonenko

Vinh

et al. 2016

PeerJ

173

226

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BackgroundViruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).MethodsHere we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses.ResultsMock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample.DiscussionTogether these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.

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“…The fact that the relationship between dissolved lipidomic structure and RNA viral reads was apparent without considering one of the potentially highest viral samples act as an accidental Monte Carlo test and strengthened our confidence in this finding. (Kimura and Tomarua, 2015;Nagasaki et al, 2004;Shirai et al, 2008;Tomaru et al, 2009;Tomaru et al, 2012;Tomaru et al, 2013).…”

Section: Shifts In the Dissolved Lipidome Across The Cruise Transect mentioning

confidence: 99%

The biogeochemistry of lipid derived infochemical signals in the ocean

Edwards¹

2016

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First evidence for the existence of pennate diatom viruses

Cited by 43 publications

References 13 publications

Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom

Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

The biogeochemistry of lipid derived infochemical signals in the ocean

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