title: Environmental bacteriophages: viruses of microbes in aquatic ecosystems.
abstract: Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.
authors.affiliation: Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université Blaise Pascal Aubière, France.
authors.forename: Télesphore
authors.initials: T
authors.lastname: Sime-Ngando
keywords: aquatic ecosystems; bacteria; biogeochemical cycling; food web dynamics; horizontal gene transfers; lysis; lysogeny; viruses
references.citation: Microb Ecol. 2012 Jul;64(1):67-78
references.pmid: 22391799
references.citation: Microb Ecol. 1998 May;35(3):235-43
references.pmid: 9569281
references.citation: FEMS Microbiol Rev. 2004 May;28(2):127-81
references.pmid: 15109783
references.citation: Appl Environ Microbiol. 2006 Jul;72(7):4893-8
references.pmid: 16820485
references.citation: Curr Opin Virol. 2013 Oct;3(5):566-71
references.pmid: 23896279
references.citation: J Bacteriol. 2002 Sep;184(17):4891-905
references.pmid: 12169615
references.citation: Science. 2014 Jan 10;343(6167):183-6
references.pmid: 24408433
references.citation: Trends Microbiol. 2013 Jan;21(1):1-5
references.pmid: 23140888
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5
references.pmid: 12384570
references.citation: Virol J. 2007 Jul 06;4:69
references.pmid: 17617913
references.citation: Nat Rev Microbiol. 2012 Jun 11;10(7):472-82
references.pmid: 22683880
references.citation: Environ Microbiol. 2007 Mar;9(3):777-88
references.pmid: 17298376
references.citation: Environ Microbiol. 2009 Nov;11(11):2935-51
references.pmid: 19840100
references.citation: Nature. 1975 Jun 26;255(5511):735-7
references.pmid: 1094307
references.citation: Environ Microbiol. 2011 Jun;13(6):1412-20
references.pmid: 21392198
references.citation: ISME J. 2013 Nov;7(11):2169-77
references.pmid: 23842650
references.citation: ISME J. 2014 May;8(5):1089-100
references.pmid: 24304672
references.citation: Nature. 1989 Aug 10;340(6233):467-8
references.pmid: 2755508
references.citation: Aquat Microb Ecol. 2009 Dec;57(3):321-341
references.pmid: 27478304
references.citation: Microb Ecol. 2007 May;53(4):631-8
references.pmid: 17345141
references.citation: Appl Environ Microbiol. 2008 May;74(9):2612-8
references.pmid: 18344351
references.citation: Appl Environ Microbiol. 1999 Jan;65(1):231-40
references.pmid: 9872784
references.citation: Appl Environ Microbiol. 1979 Apr;37(4):774-8
references.pmid: 453841
references.citation: J Microbiol Methods. 2007 Dec;71(3):212-9
references.pmid: 17897741
references.citation: Environ Microbiol. 2007 Mar;9(3):789-800
references.pmid: 17298377
references.citation: J Gen Virol. 2009 Sep;90(Pt 9):2306-16
references.pmid: 19474246
references.citation: Appl Environ Microbiol. 2000 Jun;66(6):2283-9
references.pmid: 10831400
references.citation: Microbiol Mol Biol Rev. 2000 Mar;64(1):69-114
references.pmid: 10704475
references.citation: Appl Environ Microbiol. 2006 Jun;72(6):4440-5
references.pmid: 16751565
references.citation: Nat Rev Microbiol. 2011 Feb;9(2):99-108
references.pmid: 21200397
references.citation: Nat Rev Microbiol. 2005 Jun;3(6):504-10
references.pmid: 15886693
references.citation: Arch Virol. 2007 Feb;152(2):227-43
references.pmid: 17051420
references.citation: Can J Microbiol. 2009 Feb;55(2):95-109
references.pmid: 19295641
references.citation: Environ Microbiol. 2009 Nov;11(11):2915-23
references.pmid: 19735281
references.citation: Mol Biol Evol. 2013 Aug;30(8):1843-52
references.pmid: 23645554
references.citation: Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9
references.pmid: 2112744
references.citation: ISME J. 2012 Nov;6(11):2119-27
references.pmid: 22648129
references.citation: Appl Environ Microbiol. 2011 Feb;77(4):1153-61
references.pmid: 21169428
references.citation: Appl Environ Microbiol. 2012 Feb;78(3):892-4
references.pmid: 22138992
references.citation: Microb Ecol. 2014 Feb;67(2):242-4
references.pmid: 24253663
references.citation: ISME J. 2008 Jun;2(6):579-89
references.pmid: 18521076
references.citation: Curr Biol. 2012 Dec 18;22(24):2303-12
references.pmid: 23159597
references.citation: Environ Microbiol. 2010 Nov;12(11):3035-56
references.pmid: 20662890
references.citation: Environ Microbiol. 2012 Aug;14(8):2071-86
references.pmid: 22225728
references.citation: Appl Environ Microbiol. 2007 Jul;73(14):4429-38
references.pmid: 17496133
references.citation: PLoS One. 2011 Mar 23;6(3):e17722
references.pmid: 21436882
references.citation: Cell. 2002 Jan 11;108(1):13-6
references.pmid: 11792317
references.citation: J Gen Virol. 2009 Oct;90(Pt 10):2418-2424
references.pmid: 19570956
references.citation: Adv Virus Res. 1998;51:135-201
references.pmid: 9891587
references.citation: ISME J. 2013 Mar;7(3):672-9
references.pmid: 23151645
references.citation: Microbiol Mol Biol Rev. 2004 Sep;68(3):560-602, table of contents
references.pmid: 15353570
references.citation: Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12127-32
references.pmid: 19564597
references.citation: Nature. 2009 May 14;459(7244):207-12
references.pmid: 19444207
references.citation: J Virol. 2012 Apr;86(8):4611-9
references.pmid: 22318150
references.citation: Trends Microbiol. 2010 Jan;18(1):11-9
references.pmid: 19942437
references.citation: Extremophiles. 2005 Aug;9(4):289-96
references.pmid: 15947866
references.citation: J Microbiol. 2008 Aug;46(4):364-72
references.pmid: 18758725
references.citation: Microb Ecol. 2013 Nov;66(4):906-16
references.pmid: 24061344
references.citation: ISME J. 2008 May;2(5):498-509
references.pmid: 18273065
references.citation: Nature. 1999 Jun 10;399(6736):541-8
references.pmid: 10376593
references.citation: Nature. 2005 Nov 3;438(7064):86-9
references.pmid: 16222247
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15944-9
references.pmid: 18824682
references.citation: PLoS One. 2008 Jan 23;3(1):e1456
references.pmid: 18213365
references.citation: Science. 2004 Mar 12;303(5664):1626-32
references.pmid: 15016989
references.citation: Environ Microbiol. 2010 Feb;12(2):467-79
references.pmid: 19878265
references.citation: ISME J. 2007 Aug;1(4):300-12
references.pmid: 18043641
references.citation: Environ Microbiol. 2004 Jan;6(1):1-11
references.pmid: 14686936
references.citation: Curr Biol. 1999 Dec 16-30;9(24):R914-7
references.pmid: 10607585
references.citation: Nature. 2012 Feb 26;483(7388):182-6
references.pmid: 22367545
references.citation: FEMS Microbiol Rev. 2009 Mar;33(2):295-323
references.pmid: 19243445
references.citation: ISME J. 2011 May;5(5):831-42
references.pmid: 21124489
references.citation: FEBS Lett. 1994 May 16;344(2-3):125-8
references.pmid: 8187870
references.citation: Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14390-5
references.pmid: 16980413
references.citation: ISME J. 2013 Sep;7(9):1738-51
references.pmid: 23635867
references.citation: Nature. 2003 Aug 28;424(6952):1054-7
references.pmid: 12944967
references.citation: FEMS Microbiol Ecol. 2010 Oct;74(1):83-92
references.pmid: 20608981
references.citation: PLoS One. 2013 Nov 07;8(11):e76800
references.pmid: 24244268
references.citation: J Bacteriol. 2002 Aug;184(16):4529-35
references.pmid: 12142423
references.citation: PLoS One. 2012;7(3):e33641
references.pmid: 22432038
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Nat Rev Microbiol. 2006 Nov;4(11):837-48
references.pmid: 17041631
references.citation: Appl Environ Microbiol. 2002 Mar;68(3):1290-6
references.pmid: 11872479
references.citation: Nat Rev Microbiol. 2007 Oct;5(10):801-12
references.pmid: 17853907
references.citation: Curr Opin Microbiol. 2005 Aug;8(4):444-50
references.pmid: 15979387
references.citation: J Bacteriol. 1998 Sep;180(18):4765-74
references.pmid: 9733676
references.citation: Microb Ecol. 2014 Nov;68(4):740-50
references.pmid: 24910014
references.citation: Nature. 2005 Sep 15;437(7057):356-61
references.pmid: 16163346
references.citation: Nature. 2012 Mar 04;483(7389):328-30
references.pmid: 22388815
references.citation: Theor Popul Biol. 1984 Aug;26(1):93-117
references.pmid: 6484871
references.citation: Science. 2009 Feb 13;323(5916):926-30
references.pmid: 19213916
references.citation: PLoS Biol. 2006 Nov;4(11):e368
references.pmid: 17090214
references.citation: J Virol. 1977 Feb;21(2):554-9
references.pmid: 319255
references.citation: Nature. 2008 Aug 28;454(7208):1084-7
references.pmid: 18756250
references.citation: Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2192-7
references.pmid: 10051617
references.citation: Environ Microbiol. 2013 Sep;15(9):2463-75
references.pmid: 23581698
references.citation: Trends Microbiol. 2005 Jun;13(6):278-84
references.pmid: 15936660
references.citation: Microb Ecol. 2005 Jul;50(1):64-72
references.pmid: 16052381