Abstract
Phages have serious effects on global energy and nutrient cycles. Phages actively compete for host. They can distinguish between ‘self’ and ‘non-self’ (complement same, preclude others). They process and evaluate available information and then modify their behaviour accordingly. These diverse competences show us that this capacity to evaluate information is possible owing to communication processes within phages (intra-organismic), between the same, related and different phage species (interorganismic), and between phages and non-phage organisms (transorganismic). This is crucial in coordinating infection strategies (lytic vs. lysogenic) and recombination in phage genomes. Therefore it is essential to investigate what communication of phages means and to identify the difference of the biocommunication approach to investigations that are restricted to the molecular biological perspective.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abedon ST (2009) Bacteriophage intraspecific cooperation and defection. In: Adams HT (ed) Contemporary trends in bacteriophage research. Nova Science Publishers, New York, pp 191–215
Abedon ST (2011) Communication among Phages, Bacteria and soil environments. In: Witzany G (ed) Biocommunication of soil microorganisms. Springer, Dortrecht, pp 37–65
Abedon ST (2017) Commentary: communication between viruses guides Lysis-Lysogeny decisions. Front Microbiol 8:983
Ajuebor J, Buttimer C, Arroyo-Moreno S et al (2018) Comparison of Staphylococcus phage K with close phage relatives commonly employed in phage therapeutics. Antibiotics (Basel) 7(2):E37. https://doi.org/10.3390/antibiotics7020037
Amitai G, Sorek R (2017) Intracellular signaling in CRISPR-Cas defense. Science 357(6351):550–551
Argov T, Azulay G, Pasechnek A et al (2017) Temperate bacteriophages as regulators of host behavior. Curr Opin Microbiol 38:81–87
Argov T, Sapir SR, Pasechnek A et al (2019) Coordination of cohabiting phage elements supports bacteria-phage cooperation. Nat Commun 10(1):5288
Armon R (2011) Soil Bacteria and bacteriophages. In: Witzany G (ed) Biocommunication in soil microorganisms. Springer, Dortrecht, pp 67–112
Bassler BL, Losick R (2006) Bacterially speaking. Cell 125(2):237–246
Batinovic S, Wassef F, Knowler SA et al (2019) Bacteriophages in natural and artificial environments. Pathogens 8(3):E100
Ben-Jacob E (2014) My encounters with bacteria--learning about communication, cooperation and choice. Phys Biol 11(5):053009
Berjón-Otero M, Koslová A, Fischer MG (2019) The dual lifestyle of genome-integrating virophages in protists. Ann N Y Acad Sci 1447(1):97–109
Bernheim A, Sorek R (2018) Viruses cooperate to defeat bacteria. Nature 559(7715):482–484
Bolocan AS, Upadrasta A, Bettio PHA et al (2019) Evaluation of phage therapy in the context of enterococcus faecalis and its associated diseases. Viruses 11(4):E366. https://doi.org/10.3390/v11040366
Bondy-Denomy J, Davidson AR (2014) When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol 52(3):235–242
Borges AL, Zhang JY, Rollins MF et al (2018) Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity. Cell 174(4):917–925
Bru J-L, Rawson B, Trinh C et al (2019) PQS produced by the Pseudomonas aeruginosa stress response repels swarms away from bacteriophage and antibiotics. J Bacteriol 201:e00383–e00319
Brüssow H (2018) Population genomics of bacteriophages. In: Polz M, Rajora O (eds) Population genomics: microorganisms. Population genomics. Springer, Cham, pp 297–234
Bryan D, El-Shibiny A, Hobbs Z et al (2016) Bacteriophage T4 infection of stationary Phase E. coli: life after log from a phage perspective. Front Microbiol 7:1391
Bull JJ, Regoes RR (2006) Pharmacodynamics of non-replicating viruses, bacteriocins and lysins. Proc Biol Sci 273(1602):2703–2712
Carroll-Portillo A, Lin HC (2019) Bacteriophage and the innate immune system: access and Signaling. Microorganisms 7(12):E625
Casadesús J, D’Ari R (2002) Memory in bacteria and phage. BioEssays 24(6):512–518
Cenens W, Makumi A, Mebrhatu MT et al (2013) Phage-host interactions during pseudolysogeny: lessons from the Pid/dgo interaction. Bacteriophage 3(1):e25029
Ceyssens PJ, Minakhin L, Van den Bossche A et al (2014) Development of giant bacteriophage ϕKZ is independent of the host transcription apparatus. J Virol 88(18):10501–10510
Clokie MRJ (2018) Bacterial defence molecules target viral DNA. Nature 564(7735):199–200
Cohen D, Melamed S, Millman A et al (2019) Cyclic GMP-AMP signalling protects bacteria against viral infection. Nature 574(7780):691–695
Díaz-Muñoz SL, Koskella B (2014) Bacteria-phage interactions in natural environments. Adv Appl Microbiol 89:135–183
Dimitriu T, Ashby B, Westra ER (2019) Transposition: a CRISPR way to get around. Curr Biol 29(18):R886–R889
Domingo-Calap P, Delgado-Martínez J (2018) Bacteriophages: protagonists of a post-antibiotic era. Antibiotics (Basel) 7(3)
Engelberg-Kulka H, Glaser G (1999) Addiction modules and programmed cell death and antideath in bacterial cultures. Annu Rev Microbiol 53:43–70
Erez Z, Steinberger-Levy I, Shamir M et al (2017) Communication between viruses guides lysis-lysogeny decisions. Nature 541(7638):488–493
Feiner R, Argov T, Rabinovich L et al (2015) A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat Rev Microbiol 13(10):641–650
Fillol-Salom A, Alsaadi A, Sousa JAM et al (2019) Bacteriophages benefit from generalized transduction. PLoS Pathog 15(7):e1007888
Forterre P (2013) The virocell concept and environmental microbiology. ISME J 7(2):233–236
Gallego Del Sol F, Penadés JR, Marina A (2019) Deciphering the molecular mechanism underpinning phage arbitrium communication systems. Mol Cell 74(1):59–72.e3
Górski A, Jończyk-Matysiak E, Łusiak-Szelachowska M et al (2018) Phage therapy in prostatitis: recent prospects. Front Microbiol 9:1434. https://doi.org/10.3389/fmicb.2018.01434
Górski A, Międzybrodzki R, Węgrzyn G et al (2019) Phage therapy: current status and perspectives. Med Res Rev 40:459–463. https://doi.org/10.1002/med.21593
Guerin E, Shkoporov A, Stockdale SR et al (2018) Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut. Cell Host Microbe 24(5):653–664.e6
Guglielmini J, Woo AC, Krupovic M et al (2019) Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proc Natl Acad Sci U S A 116(39):19585–19592
Hambly E, Suttle CA (2005) The viriosphere, diversity, and genetic exchange within phage communities. Curr Opin Microbiol 8(4):444–450
Harms A, Brodersen DE, Mitarai N et al (2018) Toxins, targets, and triggers: an overview of toxin-antitoxin biology. Mol Cell 70(5):768–784
Harrington LB, Burstein D, Chen JS et al (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:839–842
Hatfull GF (2015) Dark matter of the biosphere: the amazing world of bacteriophage diversity. J Virol 89:8107–8110
Hazan R, Sat B et al (2001) Postsegregational killing mediated by the P1 phage “addiction module”phd-doc requires the Escherichia coli programmed cell death system mazEF. J Bacteriol 183(6):2046–2050
Kaiser D, Losick R (1993) How and why bacteria talk to each other. Cell 73(5):873–885
Kavagutti VS, Andrei AŞ, Mehrshad M et al (2019) Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome 7(1):135
Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29(18):3742–3756
Kohlenbrander PE, Andersen RN, Blehert DS et al (2002) Communication among Oral Bacteria. Microbiol Mol Biol Rev 66:486–505
Kohlenbrander PE, Egland PG, Diaz PI et al (2005) Genome-genome interactions: bacterial communities in initial dental plaque. Trends Microbiol 13:11–15
Koonin EV, Krupovic M (2017) Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity. Curr Opin Virol 25:7–15
Koonin EV, Makarova KS (2019) Origins and evolution of CRISPR-Cas systems. Philos Trans R Soc B 374:20180087
Koonin EV, Krupovic M, Yutin N (2015) Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses. Ann N Y Acad Sci 1341:10–24
Koonin EV, Makarova KS, Wolf YI et al (2019) Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire. Nat Rev Genet 21:119–131. https://doi.org/10.1038/s41576-019-0172-9
La Scola B, Desnues C, Pagnier I et al (2008) The virophage as a unique parasite of the giant mimivirus. Nature 455(7209):100–104
Landsberger M, Gandon S, Meaden S et al (2018) Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity. Cell 174(4):908–916
Lehnherr H, Yarmolinsky MB (1995) Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci U S A 92(8):3274–3277
Lehnherr H, Maguin E, Jafri S et al (1993) Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J Mol Biol 233(3):414–428
Lima-Mendez G, Toussaint A, Leplae R (2011) A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules. Res Microbiol 162(8):737–746
Liu T, Renberg SK, Haggård-Ljungquist E (1997) Derepression of prophage P2 by satellite phage P4: cloning of the P4 epsilon gene and identification of its product. J Virol 71(6):4502–4508
Manrique P, Dills M, Young MJ (2017) The human gut phage community and its implications for health and disease. Viruses 9(6):E141
Meaden S, Capria L, Alseth E et al (2019) Transient CRISPR immunity leads to coexistence with phages. bioRxiv. https://doi.org/10.1101/2019.12.19.882027
Moelling K (2016) Nutrition and the microbiome. Ann N Y Acad Sci 1371:53–64
Mougari S, Sahmi-Bounsiar D, Levasseur A et al (2019) Virophages of Giant viruses: an update at eleven. Viruses 11(8):E733
Mruk I, Kobayashi I (2014) To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res 42(1):70–86
Mulani MS, Kamble EE, Kumkar SN et al (2019) Emerging strategies to combat ESKAPE pathogens in the era of antimicrobial resistance: a review. Front Microbiol 10:539
Nakayama K, Takashima K, Ishihara H, et al (2000) The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol 38:213–231
Ofir G, Sorek R (2018) Contemporary phage biology: from classic models to new insights. Cell 172(6):1260–1270
Paez-Espino D, Zhou J, Roux S et al (2019) Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome 7(1):157
Pirnay JP, Cooper I, Caplin J et al (2018) Silk route to the acceptance and re-implementation of bacteriophage therapy-part II. Antibiotics (basel) 7(2):35
Rehman S, Ali Z, Khan M et al (2019) The dawn of phage therapy. Rev Med Virol 29(4):e2041
Riley MA (1998) Molecular mechanisms of bacteriocin evolution. Annu Rev Genet 32:255–278
Rohde C, Wittmann J, Kutter E (2018a) Bacteriophages: a therapy concept against multi-drug-resistant Bacteria. Surg Infect 19(8):737–744. https://doi.org/10.1089/sur.2018.184
Rohde C, Resch G, Pirnay JP et al (2018b) Expert opinion on three phage therapy related topics: bacterial phage resistance, phage training and Prophages in bacterial production strains. Viruses 10(4):E178
Rohwer F, Youle M, Maughan H, et al (2014) Life in our phage world. A centennial field guide to the earth’s most diverse inhabitants. Wholon, San Diego
Roux S, Krupovic M, Daly RA et al (2019) Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nat Microbiol 4(11):1895–1906
Sakr Y, Jaschinski U, Wittebole X et al (2018) Sepsis in intensive care unit patients: worldwide data from the intensive care over nations audit. Open forum. Infect Dis Ther 5(12):ofy313. https://doi.org/10.1093/ofid/ofy313
Santajit S, Indrawattana N (2016) Mechanisms of antimicrobial resistance in ESKAPE pathogens. Biomed Res Int:2475067
Sarker SA, Berger B, Deng Y et al (2017) Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh. Environ Microbiol 19(1):237–250
Sausset R, Petit MA, Gaboriau-Rothiau V et al (2020) New insights into intestinal phages. Mucosal Immunol 13:205–215. https://doi.org/10.1038/s41385-019-0250-5
Schauder S, Bassler BL (2001) The languages of bacteria. Gen Develop 15:1468–1480
Seed KD, Lazinski DW, Calderwood SB et al (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494:489–491
Shkoporov AN, Clooney AG, Sutton TDS et al (2019) The human gut Virome is highly diverse, stable, and individual specific. Cell Host Microbe 26(4):527–541
Siringan P, Connerton PL, Cummings NJ et al (2014) Alternative bacteriophage life cycles: the carrier state of campylobacter jejuni. Open Biol 4:130200
Stanley SY, Maxwell KL (2018) Phage-encoded anti-CRISPR defenses. Annu Rev Genet 52:445–464
Stedman KM (2015) Deep recombination: RNA and ssDNA virus genes in DANN virus and host genomes. Annu Rev Virol 2(1):203–217
Stokar-Avihail A, Tal N, Erez Z et al (2019) Widespread utilization of peptide communication in phages infecting soil and pathogenic Bacteria. Cell Host Microbe 25(5):746–755
Strecker J, Ladha A, Gardner Z et al (2019) RNA-guided DNA insertion with CRISPR-associated transposases. Science 365:48–53
Tabib-Salazar A, Mulvenna N, Severinov K et al (2019) Xenogeneic regulation of the bacterial transcription machinery. J Mol Biol 431(20):4078–4092
Turner PE, Chao L (1999) Prisoner’s dilemma in an RNA virus. Nature 398(6726):441–443
van Sluijs L, van Houte S, van der Oost J, Brouns SJ et al (2019) Addiction systems antagonize bacterial adaptive immunity. FEMS Microbiol Lett 366(5):fnz047
Villarreal LP (2005) Viruses and the evolution of life. ASM Press, Washington
Villarreal LP (2009) The source of self: genetic parasites and the origin of adaptive immunity. Ann N Y Acad Sci 1178:194–232
Villarreal LP (2011) Viral ancestors of antiviral systems. Viruses 3(10):1933–1958
Villarreal L (2012a) Viruses and host evolution: virus-mediated self identity. Adv Exp Med Biol 738:185–217
Villarreal LP (2012b) The addiction module as a social force. In: Witzany G (ed) Viruses: essential agents of life. Springer, Dortrecht, pp 107–145
Villarreal LP (2015) Force for ancient and recent life: viral and stem-loop RNA consortia promote life. Ann N Y Acad Sci 1341:25–34
Villarreal LP (2016) Persistent virus and addiction modules: an engine of symbiosis. Curr Opin Microbiol 31:70–79
Villarreal LP, Witzany G (2015) When competing viruses unify: evolution, conservation, and plasticity of genetic identities. J Mol Evol 80(5–6):305–318
Villarreal LP, Witzany G (2019) That is life: communicating RNA networks from viruses and cells in continuous interaction. Ann N Y Acad Sci 1447:5–20
Wang X, Kim Y, Ma Q et al (2010) Cryptic prophages help bacteria cope with adverse environments. Nat Commun 1:147
Warwick-Dugdale J, Buchholz HH, Allen MJ et al (2019) Host-hijacking and planktonic piracy: how phages command the microbial high seas. Virol J 16(1):15
Weitz JS, Mileyko Y, Joh RI et al (2008) Collective decision making in bacterial viruses. Biophys J 95(6):2673–2680
Westra ER, Buckling A, Fineran PC (2014) CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol 12(5):317–326
Wienhold SM, Lienau J, Witzenrath M (2018) Towards inhaled phage therapy in Western Europe. Viruses 11(3):E295. https://doi.org/10.3390/v11030295
Williamson KE (2011) Soil phage ecology: abundance, distribution, and interactions with bacterial host. In: Witzany G (ed) Biocommunication in soil microorganisms. Springer, Dortrecht, pp 113–136
Witzany G (1993) Naur der Sprache – Sprache der Natur. In: Sprachpragmatische Philosophie der Biologie. Koenigshausen & Neumann, Würzburg
Witzany G (2000) Life: the communicative structure. BoD, Norderstadt
Witzany G (2009) Bacteria and viruses: communal interacting agents. In: Chauhan A, Varma A (eds) A textbook of molecular biotechnology. I.K. International Publishing, New Dehli, pp 905–914
Witzany G (2010a) Uniform categorization of biocommunication in bacteria, fungi and plants. World J Biol Chem 1(5):160–180
Witzany G (2010b) Biocommunication and natural genome editing. Springer, Dordrecht
Witzany G (ed) (2011) Biocommunication in soil microorganisms. Springer, Heidelberg
Witzany G (ed) (2012a) Biocommunication of Fungi. Springer, Dordrecht
Witzany G (ed) (2012b) Biocommunication of animals. Springer, Dordrecht
Witzany G (2014) Biological Self-Organization. IJSSS 3(2):1–11
Witzany G (2016a) The biocommunication method: on the road to an integrative biology. Comm Integr Biol 9(2):e1164374
Witzany G (2016b) Key levels of biocommunication. In: Gordon R, Seckbach J (eds) Biocommunication: sign-mediated interactions between cells and organisms. World Scientific, Singapore, pp 37–61
Witzany G (ed) (2018) Biocommunication of Archaea. Springer, Cham
Witzany G (2019) Communication is the main characteristic of life. In: Kolb V (ed) Handbook of astrobiology. CRC Press, Boca Raton, pp 91–105
Witzany G, Baluška F (eds) (2012) Biocommunication of plants. Springer, Berlin/Heidelberg
Witzany G, Nowacki M (eds) (2016) Biocommunication of ciliates. Springer, Dordrecht
Yahara K, Horie R, Kobayashi I et al (2007) Evolution of DNA double-strand break repair by gene conversion: coevolution between a phage and a restriction-modification system. Genetics 176(1):513–526
Youle M, Haynes M, Rohwer F (2012) Scratching the surface of Biology’s dark matter. In: Witzany G (ed) Viruses: essential agents of life. Springer, Dortrecht, pp 61–81
Young R (2002) Bacteriophage holins: deadly diversity. J Mol Microbiol Biotechnol 1:21–36
Acknowledgement
I want to thank Luis P. Villarreal for helpfull comments.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Witzany, G. (2020). What Does Communication of Phages Mean?. In: Witzany, G. (eds) Biocommunication of Phages. Springer, Cham. https://doi.org/10.1007/978-3-030-45885-0_1
Download citation
DOI: https://doi.org/10.1007/978-3-030-45885-0_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-45884-3
Online ISBN: 978-3-030-45885-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)