Ecology of prokaryotic viruses

• Published in: FEMS microbiology reviews Vol. 28; no. 2; pp. 127 - 181
• Main Author: Weinbauer, Markus G
• Format: Journal Article
• Language: English
• Published: Oxford, UK Elsevier B.V 01.05.2004; Blackwell Publishing Ltd; Blackwell; Oxford University Press
• Subjects: Aquatic environment; Bacteria; Bacteria - virology; Bacteriophages - physiology; Bacterioplankton; Biogeochemical cycles; Biological and medical sciences; BP, bacterial production; Cell survival; Chla, Chlorophyll a; CPS, cyanophage specific; DCM, deep chlorophyll maximum; DGGE, denaturing gradient gel electrophoresis; Diversity; DMS, dimethylsulfide; DMSP, dimethylsulfonioproprionate; DOM, dissolved organic matter; Dominant species; Ecology; EFM, epifluorescence microscopy; EPS, exopolysaccharides produced by bacteria often resulting in a capsule around cells; FCM, flow cytometry; FIC, frequency of infected cells; FLV, fluorescently labeled viruses; Food chains; Food processing; Food webs; Fundamental and applied biological sciences. Psychology; FVIC, frequency of visibly infected cells; Gene transfer; Genomics; GPCA, great plate count anomaly; HNF, heterotrophic nanoflagellates; Life cycles; LRVI, loss rates of viral infectivity; LRVP, loss rates of viral particles; Lysis; Lysogeny; Microbiology; Microorganisms; MOI, multiplicity of infection; Mortality; MPN, most probable number; Mutualism; NER, nucleotide excision repair; PAR, photosynthetic active radiation; PER, photoenzymatic repair; PFGE, pulsed‐field gel electrophoresis; PFU, plaque forming unit; Phage; Phages; PHS, phage–host system; POM, particulate organic matter; Populations; Predators; Prokaryote; Prokaryotes; Prokaryotic Cells - virology; Proteomics; RFLP, restriction fragment length polymorphism; R–M, restriction–modification (an antiphage defense mechanism); SSCP, single‐strand conformation polymorphism; TEM, transmission electron microscope; TGGE, temperature gradient gel electrophoresis; T‐RFLP, terminal restriction fragment length polymorphism; VBR, viruses to bacteria ratio; VDA, virus dilution approach; VIC, visibly infected cell; Virus; Viruses; VMP, viral mortality of prokaryotes; VPR, viral production rates; WSA, whole seawater approach; DCM, deep chlorophyll maximum; POM, particulate organic matter; Chla, Chlorophyll a; PER, photoenzymatic repair; Diversity; DGGE, denaturing gradient gel electrophoresis; DMS, dimethylsulfide; TGGE, temperature gradient gel electrophoresis; EPS, exopolysaccharides produced by bacteria often resulting in a capsule around cells; RFLP, restriction fragment length polymorphism; FCM, flow cytometry; MPN, most probable number; R–M, restriction–modification (an antiphage defense mechanism); T-RFLP, terminal restriction fragment length polymorphism; VIC, visibly infected cell; CPS, cyanophage specific; PFGE, pulsed-field gel electrophoresis; VPR, viral production rates; Bacteria; SSCP, single-strand conformation polymorphism; VDA, virus dilution approach; VMP, viral mortality of prokaryotes; DMSP, dimethylsulfonioproprionate; LRVI, loss rates of viral infectivity; FVIC, frequency of visibly infected cells; LRVP, loss rates of viral particles; PAR, photosynthetic active radiation; BP, bacterial production; FIC, frequency of infected cells; VBR, viruses to bacteria ratio; Virus; NER, nucleotide excision repair; PFU, plaque forming unit; EFM, epifluorescence microscopy; WSA, whole seawater approach; MOI, multiplicity of infection; Prokaryote; TEM, transmission electron microscope; DOM, dissolved organic matter; FLV, fluorescently labeled viruses; HNF, heterotrophic nanoflagellates; PHS, phage–host system; GPCA, great plate count anomaly; Phage
• ISSN: 0168-6445; 1574-6976; 1574-6976
• DOI: 10.1016/j.femsre.2003.08.001

The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses (`phages') in marine, freshwater and soil systems from a `virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by `killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.