Missing viruses!

Viruses have a major role in the evolution, ecology and mortality of marine ecosystems. Only in the last few decades it has been realised that the viruses in the ocean may not be dominated by DNA bacteriophages. It has been suggested that RNA viruses are extremely important in marine processes and that they have been understudied. Since the first reports of the RNA virus infecting Heterossigma akashiwo, there have been many other cases of RNA viruses found in the oceans. These RNA viruses are found with molecular surveys using primers that target RNA-dependant RNA polymerase genes and are now classified into several families including Picornavirales and Reoviridae. Metagenomic surveys show that Picornaviads seem to dominate the marine RNA viruses however, few isolates are so far available.

Up until now there have been technical difficulties with quantifying virus populations due to stain sensitivity making it hard to detect small genome single stranded viruses. This study addresses for the first time, whether RNA viruses have a substantial contribution to the overall virus population by taking a different approach and estimating the relative abundance of RNA viruses from their masses in sea water.

Samples for this study were taken from Kane’ohe Bay, Hawaii and were taken straight to the lab to be filtered through 0.22µm filter. The samples of viral communities were concentrated using iron flocculation and buoyancy density gradients. The nucleic acid was then removed from the samples using fraction analysis. Samples for RNA analysis were treated with DNAase to avoid a non-specific signal and fractions were pooled to obtain a more accurate RNA estimate and overestimation was avoided using a flourmetric assay and comparing to a control of purified known RNA virus. A metagenomic analysis was used to confirm the quantity and composition of RNA viruses in the samples.

When buoyancy was accounted for and fractions of nucleotides taken out that were thought to not be of virus origin, it was seen that there was a higher percentage of RNA than DNA viruses in the samples. The metagenomics analysis found that over half of these were most similar to known eukaryote–infecting RNA viruses, 50-57% of which were single stranded viruses mainly in the Picornvirales order. Only 0.02–1.2% were unknown double stranded RNA viruses. These findings suggest that the eukaryotic-infecting viruses are as abundant as the well-studied bacteriophages. If these RNA viruses are as dominant as this data suggests, it will have a huge impact towards our understanding of plankton ecology.
There was however, limitation in the experiment due to the use of a 0. 22µm filter and the relatively small range of virus buoyancy tested as this resulted in a large number of viruses still being unaccounted for in the samples. This shows that this study is just a first step into really understanding the magnitude of RNA viruses in the oceans. It shows that current virus detection methods may be needed for adjustment to account for even the smallest viruses, and that this is an area in which work needs to be undertaken to understand further the role of viruses in marine plankton ecology.

Steward, G. F., Culley, A. I., Mueller, J. A., Wood-Charlson, E. M., Belcaid, M., and Poisson, G. (2013). Are we missing half of the viruses in the ocean? ISME J. 7, 672–679.