Ocean Viromes
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Metagenomics is the study of genomes from environmental samples as opposed to clonal cultures grown in the laboratory. The crucial aspect of this approach to biodiversity is that there should be no sampling bias due to a failure to culture the full range of organisms present in an environment. A virus metagenome is an attempt to make a comprehensive collection of all the virus genomes present in an environment, also and this is also called a virome. In 2004 a metagenomic study of the Sargasso Sea found DNA sequences from nearly 2000 different microbial species including 148 types of bacteria never seen before. This type of investigation relies on raw computing power – a total of more than a billion base pairs of non-redundant sequence was generated, annotated, and analyzed in this study (Venter et al. 2004. Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304:66-74). A proposal to assemble a human virome has also been put forward.
A recent paper looks at the viromes of four oceans (The Marine Viromes of Four Oceanic Regions. PLoS Biol 4, November 7, 2006). Why should we care about viruses in seawater? Viruses are the most common biological entities in the marine environment. They are the major predators which control the density of other marine microbes such as bacteria and algae, thus ultimately controlling the levels of processes such as photosynthesis, carbon dioxide and nitrogen fixation. Thus indirectly, they have a major influence on fisheries and on the Earth’s climate.
Although there are quite a lot of individual virus genome sequences from the oceans, not much is known about which types of virus are present in they oceans, and how they are distributed across the planet. The latest survey looked at 184 separate assemblages of viruses collected over a decade from 68 sites in four ocean regions, the Sargasso Sea, Gulf of Mexico, the Pacific off British Columbia, and the Arctic Ocean.
A total of 1.8 billion base pairs of DNA sequence data was analyzed, and more than 90% of the sequences found were not significantly similar to any of those in the existing sequence databases. The sequence diversity in different oceans was very high, probably representing several hundreds of thousands of viruses. Interestingly, the sequence richness tended to vary on a North-South gradient, with more diversity closest to the equator, and least closest to the north pole, although the diversity was greatest off British Columbia, reflecting nutrient-rich upwelling ocean currents.
So these new results tell us that regional diversity of viruses is greater than might have been expected. What sets different virus assemblages apart is the change in abundance of the most abundant members. This tends to support the old microbiology saying, “Everything is everywhere, but, the environment selects”.
[...] Ocean Viromes [...]
[...] or the total viral genome content of the DNA found in certain biological sampling areas such as entire oceans or just in humans, so one might be forgiven for assuming that viromics was the study of entire [...]
[...] another demonstration – after the viromes of whole oceans - of the sheer brute power of modern sequencing technology and bioinformatics techniques, applied [...]