What is a virus.

A virus is a small infectious agent that replicates only inside the living cells of other organisms. Viruses can infect all types oflife forms, from animals and plants to microorganisms, including bacteria and archaea.

Approximately 5000 different viruses have been described in detail at the current time, although it is known that there are millions of distinct types.[1] Viruses are found in virtually every ecosystem on Earth, and these minute life forms are thought to be the most abundant type of biological entity.[2] The study of viruses is known as virology, a specialty within the field of microbiology.

Viruses have no ability to metabolize on their own, but depend upon a host organism for replication and manufacture of chemicals needed for such replication. Rybicki has characterized viruses as a form "at the edge of life."[3] 

Evolution

Although there is no detailed catalogue of the evolutionary relationships of viruses and hosts, certain general characterizations can be made. In such viral groups as poxviruses, papillomaviruses, and tobamoviruses, molecular taxonomy aligns generally with the genetic relationships of their hosts.[4] 

It is likely that viruses began host relationships with archaea and bacteria about two billion years ago; it has been suggested, however, that the proliferation of terrestrial vascular plants was the watershed event in evolution that enabled the explosion of numbers of viral organisms and pathways.[5]

Taxonomy

There are two complementary systems for viral taxonomy: the International Committee on Taxonomy of Viruses (ICTV) and Baltimore approaches. In the case of the ICTV taxonomy, there are five distinct orders: Caudovirales, Herpesvirales, Mononegavirales, Nidovirales, and Picornavirales. Within that hierarchy reside 82 families, 307 genera, 2083 species.[6]

David Baltimore devised an earlier system based on the method of viral messenger RNA synthesis.[7] The Baltimore scheme is founded on the mechanism of messenger RNA production. Although viruses must replicate mRNAs from their genomes to produce proteins and reproduce, distinctly different mechanisms are employed within each viral family. Viral genomes may be single (ss) or double-stranded (ds), may be RNA or DNA based, and may optionally employ reverse transcriptase (RT); furthermore single-strand RNA virus helices may be either sense (+) or antisense (−). These nuances divide viruses into seven Baltimore groups.

This Baltimore classification scheme is centered around the concept of messenger RNA replication, since viruses generate messenger RNA from their genomic coding to produce proteins and from that point replicate themselves. The resulting Baltimore groups are:
• I: dsDNA type (examples: Adenovirus, Herpesvirus, Poxvirus)
• II: ssDNA type (+)sense DNA (example: Parvovirus)
• III: dsRNA type (example: Reovirus)
• IV: (+)ssRNA type (+)sense RNA (examples: Picornavirus, Togavirus)
• V: (−)ssRNA type (−)sense RNA (examples: Orthomyxovirus, Rhabdovirus)
• VI: ssRNA-RT type (+)sense RNA with DNA intermediate to life-cycle (example: Retrovirus)
• VII: dsDNA-RT type (example: Hepadnavirus)

Morphology

The majority of viruses characteristically measure between 10 and 300 nonometers (nm), although certain filoviruses extend to a length of up to 1400 nm, with a diameter of approximately 80 nm.

A complete virus, known as a virion, consists of nucleic acid encased within an exterior protective coating of proteins termed a capsid—constructed from identical protein subunits called capsomers.

Very few viruses cannot be observed with a basic light microscope, but scanning and transmission electron microscopes can be employed to observe the virion. To increase the contrast between viruses and the background, electron-dense staining is invoked; this technique involves solutions of heavy metal salts (e.g., tungsten) that can scatter impinging electrons from regions covered with the stain. When virions are coated with positive stain, fine detail is obscured, and negative stains (of the background only) are applied to complement the positive staining observations. 

Bacteriophages

A bacteriophage is a virus that attacks a bacterium host, and is one of the most abundant organisms on our planet; they are found in soil, ocean water, aerosols, and within animal intestinal tracts. For example, as many as 900 million viruses may occur in one milliliter of seawater, situated in surface microbial matting; RNA synthesis.[8] The associated infection rate of marine bacteria may approach seventy percent.

Marine ecology and carbon cycling

Bacteriophages, in particular, have a central function in marine ecology and carbon cycling. These organisms are extremely widespread in the world's oceans, sometimes occurring in concentrations as high as 900 million bacteriophages per milliliter. Secondly, they have a very rapid attack and replication cycle, being capable of attaching and injecting genomic material into a host bacterium in a matter of minutes, and achieving genetic replication of new viruses in about 20 minutes. They are capable, therefore, of very rapid rates of multiplication in the marine environment.

Next, it is important to note that bacteriophages are highly correlated with concentrations of sewage. This is due to the presence of such bacteria as E. coli present in untreated sewage. In many world regions, large volumes of untreated sewage are discharged to the oceans. Without the ability of bacteriophages to systematically decompose the resulting high bacteria levels, not only would the bacterial concentrations be very high, but opportunity for enhanced carbon dioxide respiration at the atmosphere/ocean interface would be reduced. The outcome respiration rate for ocean absorption of atmospheric carbon is approximately three gigatons per annum,[9] which is a significant percentage of the fossil fuel combustion input to the atmosphere. Thus, further understanding of these viral processes may be key to grasping the world's carbon balance, and perhaps even making intelligent management decisions to avoid global greenhouse gas buildup. 

References:

1. M. Breitbart and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus?, Trends Microbiol., vol. 1, issue 6, pp 278-284

2. R. A. Edwards and F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol., vol 3, issue 6, pp 504–510

3. E. P. Rybicki. 1990. The classification of organisms at the edge of life, or problems with virus systematics. S Aft J Sci 86:182–186 Advances in Virus Research. 394 pages

4. Adrian J. Gibbs, Charles H. Calisher and Fernando Garcia-Arenal. 1995. Molecular basis of virus evolution. 603 pages

5. Karl Maramorosch, Frederick A. Murphy and Aaron J. Shatkin. 2003. Advances in Virus Research. 394 pages

6. International Committee on Taxonomy of Viruses. 2008. Virus Taxonomy 2008. [Retrieved on May 11, 2010]

7. David Baltimore. 1974. The strategy of RNA viruses. Harvey Lectures. vol 70, pp 57-74

K. E. Wommack and R. R. Colwell. 2000. Virioplankton: viruses in aquatic osystems Microbiol. Mol. Biol. Rev. vol. 64, issue 1, pp 69–114

8. C. A. Suttle. 2007. Marine viruses--major players in the global ecosystem. Nature Reviews. Microbiology. 5 (10):801–12