Molecular dynamics of viruses in marine ecosystems

You only have to look at an electron micrograph of a seawater sample, centrifuged at high speed onto an electron microscope grid, to appreciate the enormous morphological diversity of viruses in the sea. However, this only scratches the proverbial surface of the diversity that is actually out there. If you look at that same electron microscope grid you would be lucky if you see more than a dozen bacterial morphotypes. Despite this, microbiologists have been talking for years about how high marine bacteria diversity is, with estimates ranging from only approx. 1200 species to over one million species, based primarily on data from phylogenetic analysis of 16s rDNA. Whatever the number is, virus diversity is likely to be at least an order of magnitude higher since every microbe in the sea must have at least one virus that infects it. If you just look at the range of viruses that infect one commonly used marine cyanobacterium, Synechococcus sp. WH7803 (DC2), several studies have demonstrated that a wide range of cyanophages infect this single strain. It is likely that each virus morphotype will be representative of a huge range of genotypes. Such audacious speculation can only be backed up by adopting a similar molecular strategy that microbiologists have used which has been instrumental in changing our understanding of the composition of marine bacterial communities. Unfortunately it is impossible to develop a truly universal virus primer to detect all viruses (in the same way that 16S rDNA can detect all bacteria and archea) since there are so many different types of viruses. One look at an International Committee on Taxonomy of Viroses (ICTV) report on virus taxonomy will confirm this. Just basic taxonomic criteria such as the nucleic acid characteristics: ds and ss DNA, ds RNA, negative, ambisense, positive sense ssRNA and reverse transcribing virus taxonomic orders reveal the enormous diversity. So as virological ecologists, we must take a step back, lower our sights and focus on a more realistic aim. Rather than trying to determine overall diversity of marine virus communities we can use similar molecular approaches to investigate the diversity of specific groups of viruses and determine what effect this diversity has on the dynamics and ecological functioning of the hosts they infect. Since marine virologists do not have an extensive 16S rDNA database equivalent to hand for the development of specific diagnostic virus probes, research into identifying s