Are we missing half the viruses in the ocean?

Are we missing half the viruses in the ocean?

It has been assumed most seawater viruses that infect bacteria contain DNA, however the quantity of RNA infecting bacteria has never been measured. Viruses influence the ecology, evolution and mortality of plankton and there is increasing indication that there are a diverse range of RNA viruses that infect important members of the marine plankton food web. Therefore, this study was important in gaining a better understanding of marine viral dynamics, especially as RNA viruses predominantly target eukaryotes.  

The reason for there being little knowledge about the abundance of RNA viruses in the ocean is due to difficulties in the technical methods required to achieve this. Studies investigating the abundance of DNA viruses have previously used fluorescence techniques, however it has been found that as the stains differ in sensitivity, some are unable to detect individual virions that have a very small genome. Therefore, this study instead measured the relative mass of DNA and RNA and coupled this with estimates of the nucleic acid mass for each in order to calculate an abundance of marine RNA viruses.

The seawater samples were taken from Kāne Bay in Hawaii and immediately taken to the laboratory where they were filtered at 0.22μm and purified. A fraction analysis was then conducted and the nucleic acid from each sample removed. The study used fluorometry, as this provided the sensitivity required to assay the nucleic acids, and measured the DNA and RNA contents from each fraction separately. In order to prevent overestimation of the abundance of viral RNA they also used spectrophotometry to measure the mass of RNA and compared the results obtained from the fluorometry. Metagenomic analysis was applied to verify the RNA composition. This gave rise to specific ranges of RNA density, which were used to estimate the quantity of RNA virus genomes.

Due to losses encountered during the study, the number of viruses in the final sample was a minimal estimate and it was assumed this loss was similar for both DNA and RNA viruses. One of the main limitations to the methods was the fact that the filter used was 0.2μm, meaning some viruses were lost at the beginning stages of the study, perhaps causing bias against DNA viruses, since the largest known viruses contain double stranded DNA. Furthermore, they stated that the viral concentration method used was only tested on DNA, and just assumed that it would be as efficient for RNA viruses. This, combined with the fact they were more hesitant to allocate RNA than DNA viruses suggests the results may be biased towards DNA viruses.

Nonetheless, the findings from this study demonstrated that RNA viruses were more abundant than DNA viruses. The most dominant species present, with 50-57% of the reads from the viral fractions, were RNA viruses that infect eukaryotes, most of which were of the order Picornavirales, which other studies have found to be very diverse in seawater. Although there is a smaller concentration of eukaryotic plankton than bacteria in the ocean, these results suggest that eukaryotic viruses are as abundant as bacteriophages. Therefore if these results are a correct representation, it could have a large impact on the understanding of marine viral ecology.

This study provides evidence that the current fluorescence based methods employed to measure virus abundance may need modification in order to allow the smallest of viruses to be included in these counts. The method used in this study provides an estimate of the contribution of RNA viruses in the ocean and could be utilised to validate whether this is also representative of other marine habitats.

Grieg F Steward^1,3, Alexander I Culley^1,3, Jaclyn A Mueller¹, Elisha M Wood-Charlson^1,4, Mahdi Belcaid² and Guylaine Poisson²

The ISME Journal advance online publication 15 November 2012; doi: 10.1038/ismej.2012.121