Ecology of prokaryotic viruses

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...

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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
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Abstract	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.
AbstractList	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. Abstract 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.
Author	Weinbauer, Markus G
Author_xml	– sequence: 1 givenname: Markus G surname: Weinbauer fullname: Weinbauer, Markus G email: markus.weinbauer@obs-vlfr.fr organization: Department of Biological Oceanography, Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
BackLink	http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=15701246$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/15109783$$D View this record in MEDLINE/PubMed
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Issue	2
Keywords	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
Language	English
License	CC BY 4.0
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PMID	15109783
PQID	2333586849
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PageCount	55
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PublicationCentury	2000
PublicationDate	May 2004
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PublicationPlace	Oxford, UK
PublicationPlace_xml	– name: Oxford, UK – name: Oxford – name: England – name: Delft
PublicationTitle	FEMS microbiology reviews
PublicationTitleAlternate	FEMS Microbiol Rev
PublicationYear	2004
Publisher	Elsevier B.V Blackwell Publishing Ltd Blackwell Oxford University Press
Publisher_xml	– name: Elsevier B.V – name: Blackwell Publishing Ltd – name: Blackwell – name: Oxford University Press
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11 Jain, Rivera, Lake (BIB475) 1999; 96 Tilman (BIB496) 1996; 77 Proctor (BIB31) 1998 DeLong, Franks, Alldregde (BIB371) 1993; 38 Jiang, Paul (BIB381) 1998; 35 Steward (BIB148) 2001; Vol. 30 Weinbauer, Suttle (BIB88) 1996; 62 Ogunseitan, Sayler, Miller (BIB129) 1992; 58 Larsen, Castberg, Sandaa, Brussaard, Egge, Heldal, Paulino, Thyrhaug, van Hannen, Bratbak (BIB224) 2001; 221 Doermann (BIB267) 1948; 55 Paul (BIB19) 2000 Yamasaki, Fukuda, Fukuda, Miyajima, Nagata, Ogawa, Koike (BIB368) 1998; 43 Jürgens, Pernthaler, Schalla, Amann (BIB239) 1999; 65 Wilhelm, Weinbauer, Suttle, Pledger, Mitchell (BIB222) 1998; 14 Karentz, Bothwell, Coffin, Hanson, Herndl, Kilham, Lesser, Lindell, Moeller, Morris, Neale, Sanders, Weiler, Wetzel (BIB308) 1994; 43 Middelboe, Jørgensen, Kroer (BIB423) 1996; 62 Bratbak, Haslund, Heldal, Næss, Røeggen (BIB154) 1992; 85 Hara, Koike, Terauchi, Kamiya, Tanoue (BIB205) 1996; 145 Hurst (BIB15) 2000 Sieburth (BIB369) 1987 Li, Rao, Harrison, Smith, Cullen, Irvin, Platt (BIB438) 1983; 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Snippet	The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with... Abstract The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is...
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SubjectTerms	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
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Title	Ecology of prokaryotic viruses
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