Phage ecology/Bibliography

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A list of key readings about Phage ecology.
Please sort and annotate in a user-friendly manner. For formatting, consider using automated reference wikification.

Provided are suggested readings gleaned mostly from the secondary literature, presented by category. When available, links are being provided to full text, online versions of articles, or to abstracts if full text versions are not available. Avoided are linking directly to PDFs or to materials posted on personal web sites, unless the latter is where an article was "published". An approximation of ASM (American Society for Microbiology) conventions are used throughout. Some articles may be found online on personal web pages[1]. An extensive list of phage monographs also exists, though these do not by and large have a strong phage ecology emphasis.

General Reviews

These are articles that provide a good overview of general aspects phage ecology.

  • Abedon, S. T. 2006. Phage ecology, p. 37-46. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-19-514850-9
  • Breitbart, M., F. Rohwer, and S. T. Abedon. 2005. Phage ecology and bacterial pathogenesis, p. 66-91. In M. K. Waldor, D. I. Friedman, and S. L. Adhya (eds.), Phages: Their Role in Bacterial Pathogenesis and Biotechnology. ASM Press, Washington DC. ISBN 1-55581-307-0
  • Brüssow, H., and E. Kutter. 2005. Phage ecology, p. 129-164. In E. Kutter and A. Sulakvelidze (eds.), Bacteriophages: Biology and Application. CRC Press, Boca Raton, Florida. ISBN 0-8493-1336-8
  • Chibani-Chennoufi, S., A. Bruttin, M. L. Dillmann, and H. Brüssow. 2004. Phage-host interaction: an ecological perspective. J. Bacteriol. 186:3677-3686. full text
  • Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127-181. abstract
  • Paul, J. H., and C. A. Kellogg. 2000. Ecology of bacteriophages in nature, p. 211-246. In C. J. Hurst (ed.), Viral Ecology. Academic Press, San Diego. ISBN 0-12-362675-7
  • Levin, B. R., and Richard Lenski. 1985. Bacteria and phage: A model system for the study of the ecology and co-evolution of hosts and parasites, p. 227-242. In D. Rollinson and R. M. Anderson (eds.), Ecology and Genetics of Host-Parasite Interactions. Academic Press, London. ISBN 0-12-593690-7
  • Anderson, E. S. 1957. The relations of bacteriophages to bacterial ecology, p. 189-217. In R. E. O. Williams and C. C. Spicer (eds.), Microbial Ecology. Cambridge University Press, London.

Books

A handful of books provide a good (if in many cases dated) overview of various aspects of phage ecology.

  • Abedon, S. T. (2007=scheduled publication date, and we are on schedule!). Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses. Cambridge University Press, Cambridge, UK.
  • Ackermann, H.-W., and M. S. DuBow. 1987. Viruses of Prokaryotes, Volume 1, General Properties of Bacteriophages. CRC Press, Boca Raton, Florida. ISBN 0-8493-6056-0
  • Ackermann, H.-W., and M. S. DuBow. 1987. Viruses of Prokaryotes, Volume 2, Natural Groups of Bacteriophages. CRC Press, Boca Raton, Florida. ISBN 0-8493-6056-0
  • Goyal, S. M., C. P. Gerba, and G. Bitton. 1987. Phage Ecology. CRC Press, Boca Raton, Florida. ISBN 0-471-82419-4

Phage "organismal" ecology (suggested reading)

None of these reviews are devoted exclusively to issues of phage "organismal" ecology, but of those reviews of phage ecology, these cover that subject most extensively. See virulence evolution, etc., on the phage experimental evolution page for additional references. Return to phage "organismal" ecology.

  • Abedon, S. T. 2006. Phage ecology, p. 37-46. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-19-514850-9
  • Breitbart, M., F. Rohwer, and S. T. Abedon. 2005. Phage ecology and bacterial pathogenesis, p. 66-91. In M. K. Waldor, D. I. Friedman, and S. L. Adhya (eds.), Phages: Their Role in Bacterial Pathogenesis and Biotechnology. ASM Press, Washington DC. ISBN 1-55581-307-0
  • Brüssow, H., and E. Kutter. 2005. Phage ecology, p. 129-164. In E. Kutter and A. Sulakvelidze (eds.), Bacteriophages: Biology and Application. CRC Press, Boca Raton, Florida. ISBN 0-8493-1336-8
  • Chibani-Chennoufi, S., A. Bruttin, M. L. Dillmann, and H. Brüssow. 2004. Phage-host interaction: an ecological perspective. J. Bacteriol. 186:3677-3686. full text
  • Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127-181. abstract
  • Paul, J. H., and C. A. Kellogg. 2000. Ecology of bacteriophages in nature, p. 211-246. In C. J. Hurst (ed.), Viral Ecology. Academic Press, San Diego. ISBN 0-12-362675-7
  • Robb, F. T., and R. T. Hill. 2000. Bacterial viruses and hosts: Influence of culturable state, p. 199-208. In R. R. Colwell and D. J. Grimes (eds.), Nonculturable Microorganisms in the Environment. ASM Press, Washington, D.C. ISBN 1-55581-196-5
  • Schrader, H. S., J. O. Schrader, J. J. Walker, N. B. Bruggeman, J. M. Vanderloop, J. J. Shaffer, and T. A. Kokjohn. 1997. Effects of host starvation on bacteriophage dynamics, p. 368-385. In R. Y. Morita (ed.), Bacteria in Oligotrophic Environments. Starvation-Survival Lifestyle. Chapman & Hall, New York. ISBN 0-412-10661-2
  • Kutter, E., E. Kellenberger, K. Carlson, S. Eddy, J. Neitzel, L. Messinger, J. North, and B. Guttman. 1994. Effects of bacterial growth conditions and physiology on T4 infection, p. 406-418. In J. D. Karam (ed.), The Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC. ISBN 1-55581-064-0
  • Herskowitz, I., and F. Banuett. 1984. Interaction of phage, host, and environmental factors in governing the λ lysis-lysogeny decision, p. 59-73. In V. L. Chopra, B. C. Joshi, R. P. Sharma, and H. C. Bansal (eds.), Genetics, New Frontier: Proceedings of the XV International Congress of Genetics. Oxford and I.B.H., New Delhi.
  • Lwoff, A. 1953. Lysogeny. Bacteriol. Rev. 17:269-337. full text

Phage "organismal" experimental protocols (suggested reading)

It is important to characterize phages "organismally". A number of protocols have been published. Additional phage protocols should be available before the end of 2007. Return to phage "organismal" ecology methods.

  • Carlson, K. 2005. Working with bacteriophages: common techniques and methodological approaches, p. 437-494. In E. Kutter and A. Sulakvelidze (eds.), Bacteriophages: Biology and Application. CRC Press, Boca Raton, Florida. ISBN 0-8493-1336-8
  • Carlson, K., and E. S. Miller. 1994. Enumerating phage: the plaque assay, p. 427-429. In J. D. Karam (ed.), Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC. ISBN 1-55581-064-0
  • Carlson, K., and E. S. Miller. 1994. General procedures, p. 427-437. In J. D. Karam (ed.), Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC. ISBN 1-55581-064-0
  • Carlson, K. 1994. Single-step growth, p. 434-437. In J. D. Karam (ed.), Molecular Biology of Bacteriophage T4. ASM Press, Washington. ISBN 1-55581-064-0
  • Snustad, D. P., and D. S. Dean. 1971. Genetics Experiments with Bacterial Viruses. W. H. Freeman and Co., San Francisco. ISBN 0-7167-0161-8
  • Eisenstark, A. 1967. Bacteriophage techniques. Methods in Virology 1:449-524.
  • Adams, M. H. 1959. Bacteriophages. Interscience, New York.

Phage population ecology (suggested reading)

There are very few reviews on phage ecology that spend much time emphasizing phage population ecology, published at least. Anticipate better than a doubling of the number before the end of 2007. Return to phage population ecology.

  • Abedon, S. T. 2006. Phage ecology, p. 37-46. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-19-514850-9
  • Bull, J. J., D. W. Pfening, and I.-W. Wang. 2004. Genetic details, optimization, and phage life histories. Trends Ecol. Evol. 19:76-82. abstract & pay article

Phage community ecology (suggested reading)

Having received the most attention from both experimentalists and theoreticians among the various phage ecologies, a relatively large number of phage ecology reviews exist. Note that much of this literature has been motivated more from the bacterial rather than explicitly the phage perspective. See coevolution on the phage experimental evolution page for additional references. Return to phage community ecology.

  • Abedon, S. T. 2006. Phage ecology, p. 37-46. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-19-514850-9
  • Abedon, S. T., and J. T. LeJeune. 2005. Why bacteriophage encode exotoxins and other virulence factors. Evolutionary Bioinformatics Online 1:97-110. full text
  • Comeau, A. M., and H. M. Krisch. 2005. War is peace--dispatches from the bacterial and phage killing fields. Curr. Opin. Mirobiol. 8:488-494. abstract & pay article
  • Weinbauer, M. G., and F. Rassoulzadegan. 2004. Are viruses driving microbial diversification and diversity? Environmental Microbiology 6:1-11. abstract
  • Levin, B. R., and J. J. Bull. 2004. Population and evolutionary dynamics of phage therapy. Nat. Rev. Microbiol. 2:166-173. abstract
  • Sutherland, I. W., K. A. Hughes, L. C. Skillman, and K. Tait. 2004. The interaction of phage and biofilms. FEMS Microbiol. Lett. 232:1-6. abstract
  • Bohannan, B. J. M., and R. E. Lenski. 2000. Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage. Ecol. Lett. 3:362-377. full text
  • Suttle, C. A. 1994. The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28:237-243. abstract & pay article
  • Miller, R. V., and G. S. Sayler. 1992. Bacteriophage-host interactions in aquatic systems, p. 176-193. In E. M. H. Wellington and J. D. van Elsas (eds.), Genetic Interactions among Microorganisms in the Natural Environment. Pergamon Press, Oxford. ISBN 0-08-042000-1
  • Lenski, R. E. 1988. Dynamics of interactions between bacteria and virulent bacteriophage. Adv. Microbial. Ecol. 10:1-44.
  • Levin, B. R., and R. E. Lenski. 1985. Bacteria and phage: A model system for the study of the ecology and co-evolution of hosts and parasites, p. 227-242. In D. Rollinson and R. M. Anderson (eds.), Ecology and Genetics of Host-Parasite Interactions. Academic Press, London. ISBN 0-12-593690-7
  • Krüger, D. H., and T. A. Bickle. 1983. Bacteriophage survival: Multiple mechanisms for avoiding deoxyribonucleic acid restriction systems of their hosts. Microbiol. Rev. 47:345-360. full text
  • Levin, B. R., and R. E. Lenski. 1983. Coevolution in bacteria and their viruses and plasmids, p. 99-127. In D. J. Futuyama and M. Slatkin (eds.), Coevolution. Sinauer Associates, Inc., Sunderland, Massachusetts. ISBN 0-87893-229-1
  • Barksdale, L., and S. B. Ardon. 1974. Persisting bacteriophage infections, lysogeny, and phage conversions. Ann. Rev. Microbiol. 28:265-299. abstract & pay article
  • Anderson, E. S. 1957. The relations of bacteriophages to bacterial ecology, p. 189-217. In R. E. O. Williams and C. C. Spicer (eds.), Microbial Ecology. Cambridge University Press, London.

Phage ecosystem ecology (suggested reading)

The majority (if not all!) reviews with a phage ecosystem ecology emphasis also emphasize aquatic phage ecology. The following are examples. Return to phage ecosystem ecology.

  • Weinbauer, M. G. 2004. Ecology of Prokaryotic Viruses. FEMS Microbiol. Rev. 28:127-181. abstract
  • Wommack, K. E., and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114. full text
  • Suttle, C. A. 2000. Cyanophages and their role in the ecology of cyanobacteria, p. 563-589. In B. A. Whitton and M. Potts (eds.), The Ecology of Cyanobacteria: Their Diversity in Time and Space. Kluwer Academic Publishers, Boston. ISBN 0-7923-4735-8
  • Suttle, C. A. 2000. The ecology, evolutionary and geochemical consequences of viral infection of cyanobacteria and eukaryotic algae, p. 248-286. In C. J. Hurst (ed.), Viral Ecology. Academic Press, New York. ISBN 0-12-362675-7
  • Fuhrman, J. A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature 399:541-548. abstract & pay article
  • Wilhelm, S. W., and C. A. Suttle. 1999. Viruses and nutrient cycles in the sea. BioScience 49:781-788. full text
  • Bratbak, G., T. F. Thingstad, and M. Heldal. 1994. Viruses and the microbial loop. Microb. Ecol. 28:209-221. abstract & pay article
  • Fuhrman, J. A., R. M. Wilcox, R. T. Noble, and N. C. Law. 1993. Viruses in marine food webs, p. 295-298. In R. Guerrero and C. Pedros-Alio (eds.), Trends in microbial ecology. Spanish Society for Microbiology, Barcelona.
  • Thingstad, T. F., M. Heldal, G. Bratbak, and I. Dundas. 1993. Are viruses important partners in pelagic food webs? Trends Ecol. Evol. 8:209-213. abstract
  • Fuhrman, J. A. 1992. Bacterioplankton roles in cycling of organic matter: the microbial food web, p. 361-383. In P. G. Falkowski and A. D. Woodhead (eds.), Primary Productivity and Biogeochemical Cycles in the Sea. Plenum, New York. ISBN 0-306-44192-6

Terrestrial phage ecology (suggested reading)

Not nearly as well developed as aquatic phage ecology, due to the complexity and heterogensity of solid phase versus liquid phage, terrestrial phage ecology has been explored in a number of reviews. The following are suggested readings.

  • Gill, J. J., and S. T. Abedon. 2003. Bacteriophage ecology and plants. APSnet feature. full text
  • Williams, S. T., A. M. Mortimer, and J. Eccleston. 1994. Bacteriophages in soil, p. 121R. Webster and A. Granoff (eds.), Encyclopedia of Virology. Academic Press.
  • Williams, S. T., A. M. Mortimer, and L. Manchester. 1987. Ecology of soil bacteriophages, p. 157-179. In S. M. Goyal, C. P. Gerba, and G. Bitton (eds.), Phage Ecology. John Wiley & Sons, New York. ISBN 0-471-82419-4
  • Williams, S. T., and S. Lanning. 1984. Studies of the ecology of streptomycete phage in soil, p. 473-483. In L. Ortiz-Ortiz, L. F. Bojalil, and V. Yakoleff (eds.), Biological, Biochemical and Biomedical Aspects of Actinomycetes. Academic Press, London. ISBN 0-12-528620-1
  • Anderson, E. S. 1957. The relations of bacteriophages to bacterial ecology, p. 189-217. In R. E. O. Williams and C. C. Spicer (eds.), Microbial Ecology. Cambridge University Press, London.

The following deals more with phage (and other virus) retention in soils more than phage ecology per se.

  • Duboise, S. M., B. E. Moore, C. A. Sorber, and B. P. Sagik. 1979. Viruses in soil systems, p. 245-285. In H. D. Isenberg (ed.), CRC Critical Reviews in Microbiology. CRC Press, Boca Raton, FL.

Aquatic phage ecology (suggested reading)

Aquatic phage ecology came to dominate phage ecology stemming from the seminal publication by Bergh et al. in 1989 (Bergh, O., K. Y. Børsheim, G. Bratbak, and M. Heldal. 1989. High abundance of viruses found in aquatic environments. Nature 340:467-468.). A large number of publications, and a large number reviews followed. The latter are listed below, exclusive of those listed above under the heading of Phage ecosystem ecology (suggested reading). See also cyanophage for additional references.

  • Mann, N. H. 2006. Phages of cyanobacteria, p. 517-533. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-471-82419-4
  • Miller, R. V. 2006. Marine phages, p. 534-544. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-471-82419-4
  • Brüssow, H., and E. Kutter. 2005. Phage ecology, p. 129-164. In E. Kutter and A. Sulakvelidze (eds.), Bacteriophages: Biology and Application. CRC Press, Boca Raton, Florida. ISBN 0-8493-1336-8
  • Paul, J. H., and M. B. Sullivan. 2005. Marine phage genomics: what have we learned? Curr. Opin. Biotechnol. 16:299-307. abstract & pay article
  • Fuhrman, J. A., and M. Schwalbach. 2003. Viral influence on aquatic bacterial communities. Biol. Bull. 204:192-195. full text
  • Paul, J. H., M. B. Sullivan, A. M. Segall, and F. Rohwer. 2002. Marine phage genomics. Comparative Biochemistry and Physiology 133:463-476.
  • Suttle, C. A. 2002. Community structure: viruses, p. 364-370. In C. J. Hurst, G. R. Knudson, M. J. McInerney, L. D. Stezenbach, and M. V. Walter (eds.), Manual of Environmental Microbiology (2nd Edition). ASM Press, Washington, DC.
  • Fuhrman, J. A. 2000. Impact of viruses on bacterial processes, p. 327-350. In D. L. Kirchman (ed.), Microbial Ecology of the Oceans. Wiley & Sons, New York.
  • Martin, E. L., and T. A. Kokjohn. 1999. Cyanophages, p. 324-332. In A. Granoff and R. G. Webster (eds.), Encyclopedia of Virology second edition. Academic Press, San Diego.
  • Suttle, C. A. 1999. Do viruses control the oceans? Nat. His. 108:48-51.
  • Proctor, L. M. 1998. Marine virus ecology, p. 113-130. In S. E. Cooksey (ed.), Molecular Approaches to the Study of the Ocean. Chapman & Hall, London.
  • Proctor, L. M. 1997. Advances in the study of marine viruses. Microscopy Research and Technique 37:136-161.
  • Suttle, C. A. 1997. Community structure: viruses, p. 272-277. In C. J. Hurst, G. R. Knudson, M. J. McInerney, L. D. Stezenbach, and M. V. Walter (eds.), Manual of Environmental Microbiology. ASM Press, Washington DC.
  • Paul, J. H., C. A. Kellogg, and S. C. Jiang. 1996. Viruses and DNA in marine environments, p. 119-128. In R. R. Colwell, U. Simidu, and K. Ohwada (eds.), Microbial Diversity in Time and Space. Plenum Press, New York, N.Y.
  • Suttle, C. A. 1994. The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28:237-243.
  • Bratbak, G., M. Heldal, A. Naess, and T. Roeggen. 1993. Viral impact on microbial communities, p. 299-302. In R. Guerrero and C. Pedros-Alio (eds.), Trends in Microbial Ecology. Spanish Society for Microbiology, Barcelona.
  • Fuhrman, J. A., and C. A. Suttle. 1993. Viruses in marine planktonic systems. Oceanography 6:50-62.
  • Thingstad, T. F., M. Heldal, G. Bratbak, and I. Dundas. 1993. Are viruses important partners in pelagic food webs? Trends Ecol. Evol. 8:209-213.
  • Miller, R. V., and G. S. Sayler. 1992. Bacteriophage-host interactions in aquatic systems, p. 176-193. In E. M. H. Wellington and J. D. van Elsas (eds.), Genetic Interactions among Microorganisms in the Natural Environment. Pergamon Press, Oxford.
  • Cannon, R. E. 1987. Cyanophage ecology, p. 245-265. In S. M. Goyal, C. P. Gerba, and G. Bitton (eds.), Phage Ecology. John Wiley & Sons, New York.
  • Farrah, S. R. 1987. Ecology of phage in freshwater environments, p. 125-136. In S. M. Goyal, G. P.
  • Moebus, K. 1987. Ecology of marine bacteriophages, p. 137-156. In S. M. Goyal, G. P. Gerba, and G. Bitton (eds.), Phage Ecology. John Wiley & Sons, New York.
  • Cannon, R. E., M. S. Shange, and E. DeMichele. 1974. Ecology of blue-green algal viruses. J. Environ. Eng. Div. , ASCE 100:1205-1211.
  • Shilo, M. 1972. The ecology of cyanophages. Bamidgeh 24:76-82.
  • Spencer, R. 1963. Bacterial viruses in the sea, p. 350-365. In C. H. Oppenheimer (ed.), Symposium on Marine Microbiology. Charles C. Thomas, Publisher, Springfield, IL.

Other environments (suggested reading)

  • Bogosian, G. 2006. Control of bacteriophage contamination in commercial microbiology and fermentation facilities, p. 667-673. In R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. ISBN 0-19-514850-9
  • Moineau, S., and C. Lévesque. 2005. Control of bacteriophages in industrial ferments, p. 285-296. In E. Kutter and A. Sulakvelidze (eds.), Bacteriophages: Biology and Application. CRC Press, Boca Raton, Florida. ISBN 0-8493-1336-8
  • Sanders, M. E. 1987. Bacteriophages of industrial importance, p. 211-244. In S. M. Goyal, G. P. Gerba, and G. Bitton (eds.), Phage Ecology. John Wiley & Sons, New York. ISBN 0-471-82419-4
  • Many PDF- (or, alternatively, HTML-) based articles are online through PubMed or via the web sites of open access journals such as those published by BioMed Central. Alternativley, they may be posted on "private" web sites (perhaps in copyright violation) by authors or other individuals. Consequently, it is often possible to find an article by doing a Google search on article titles. You can sometimes increase useful hits by placing titles in quotes, adding author last names (outside of quotes), or by limiting searches to PDF documents.