Marine Viruses Grieg F Steward, Alexander I Culley, and Elisha M Wood-Charlson, University of Hawaii at Manoa, Honolulu, HI, USA r 2013 Elsevier Inc All rights reserved Glossary Bacteriophage A virus that infects a bacterium Cyanophage A virus that infects a cyanobacterium Lysogen A bacterium which has a temperate virus integrated into its genome So called because it may lyse at some later time as a result of the virus excising from the genome and initiating replication (induction) This occurs spontaneously with low probability or with high probability in response to a stress to the host cell Lytic virus A virus for which the usual or only mode of replication is through synthesis of new virions and lysis of the host cell Plasmid A piece of DNA (usually circular) that can replicate independently of the chromosome of a cell and which codes for supplementary (noncore) functions The Discovery of Viruses The agents of viral diseases were being studied by some eminent microbiologists such as Louis Pasteur, by at least the 1880s, but the truly unique character of these infectious agents was not fully appreciated for some time The first clue that viruses were not like other known pathogens came from experiments conducted independently in the 1890s by the Russian scientist Dmitri Ivanovsky and the Dutch scientist Martinus Beijerinck on a disease causing agent in tobacco plants in the 1890s These scientists discovered that sap from infected plants retained its infectivity even after passage through filters with pores small enough to remove bacteria This filtration test became the basis for assigning other pathogens to this new operationally defined class referred to as ‘‘filterable agents’’ (Levine and Enquist, 2007) In the subsequent 114 years, the study of viruses has not only led to a detailed understanding of their molecular nature, diversity, and ecology, it has resulted in the elucidation of some of the fundamental processes of cells in a new field of research (molecular biology), and led to relief from some of the most virulent diseases known to humankind Some landmarks in virology at the beginning of the twentieth century included the discovery and identification of the viral agents of diseases such as yellow fever, influenza, rabies, and polio, and the realization that viruses were involved in some types of cancer The discovery that bacteria are also susceptible to viral infections was discovered independently by Frederick Twort in 1915 and Felix d’Herelle in 1917 The first clear proof that viruses are particles and not a fluid was provided by d’Herelle’s experiments in which he showed that dilutions of the lytic agent resulted in discrete zones of lysis on a lawn of bacteria This was later confirmed with the application of electron microscopy (1939) and X-ray crystallography (1941) to the analysis Encyclopedia of Biodiversity, Volume Temperate virus A virus for which there is a high probability that the viral genome will reside passively in the host cell, sometimes by integrating its genome into the host genome, rather than initiating a lytic infection, thereby creating a lysogen or a persistent infection Transposon A DNA sequence that can transpose itself, or a copy of itself, from one location to another within a larger segment of DNA or from one molecule of DNA to another Also referred to as ‘‘jumping genes.’’ -virad A suffix denoting viruses that belong to an order of viruses (e.g., viruses in the order Picornavirales are picornavirads) -virid A suffix denoting viruses that belong to a family (e.g., viruses belonging to the family Phycodnaviridae are picornavirids) Virion An individual viral particle of viruses, which provided the first detailed views of the structure of viruses The relative simplicity of bacteriophages, and the ease with which they could be propagated in the lab under controlled conditions, made them an attractive model system for the nascent field of molecular biology Work with bacteriophages resulted in the demonstration that nucleic acids, not proteins, were the repository for genetic information (1950s), the elucidation of the mechanisms of gene regulation and of the triplet code of genes (1960s), and the development of tools that led to recombinant DNA technology (1970s) The first genome to be sequenced was that of the RNA-containing bacteriophage, MS2, in 1976, followed by the DNA genome of bacteriophage, øX174, in 1977 These were the inaugural events in the genomics revolution in biology The number of viral genomes completely sequenced is now in the thousands and rising rapidly Viruses and Biodiversity In the context of biodiversity, viruses occupy a curious position Since they are not organisms per se, they might be considered exempt from the discussion However, they are extraordinarily diverse biological entities, both genotypically and phenotypically, and have been instrumental in promoting biodiversity among all cellular life forms Viruses are clearly distinct from the cellular life on which they depend for replication in several important respects (Lwoff, 1957) the most salient being that they replicate by assembly rather than division (Figure 1) They are, in essence, molecular symbionts of cells, but unlike other molecular symbionts, such as plasmids and transposons, they package their genome in a protein shell (capsid) for efficient dispersal outside of a cell Encapsidation serves to protect the viral nucleic acid from degradation in the http://dx.doi.org/10.1016/B978-0-12-384719-5.00401-9 127