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Bacteriophage Ecology Group News - - - - - - - - - - - - - - - - - - - - @ www.phage.org by Stephen T. Abedon (editor) December 1, 2006 issue (#25) |
Stephen T. Abedon, The Ohio State University
Bacteriophage Ecology Group News (BEG News) 25
In this day of search engines—and increasing expectation by students, the public, and academics alike for finding answers to questions online—an effective, dynamic, and permanent presence on the World Wide Web is important, if not crucial, for the maintenance of coherence, efficiency, effectiveness, and outreach by academic disciplines. Phage ecology is one such discipline, and toward establishing a web presence we have BEG and BEG News. Unfortunately, as the absence of BEG News from your lives for over a year and a half is testament, maintaining a web presence, especially by one person, is pretty difficult and time consuming. It also places the online “defining” of a discipline into too few hands, plus lacks a certain permanence that academics prefer, and should demand. Who, after all, is going to keep BEG alive after I’m gone?
In effect, every discipline faces these problems, and some no doubt have solved them. Solutions, however, tend to be ad hoc. Should every academic discipline re-invent the wheel to develop their own, personal online presence? Should we all be hiring IT people to produce technologically effective web sites that we then endow and seek to maintain for eternity? Should we all just sit on information that might otherwise be useful to our colleagues—knowledge of patents, interesting web sites, obscure references, laboratory subtleties, etc.—just because they are not readily published in traditional venues? To all these questions I say, “No!”. Publishing is (very) important but still is a very limited means of disseminating information. Combinations of mailing and photocopying (or mimeographing) have been employed in the past to transcend the problem that we can’t publish everything, and that we can accomplish only so much in terms of information dissemination through travel, such as to meetings. Personal web pages, or even those of societies, have supplanted earlier, paper-based attempts at self publishing, and are hugely powerful due to modern search engines. Nevertheless, personal web pages suffer from the problems outlined above: Too few people are responsible for maintaining (too-little) information that is too labile and otherwise impermanent.
The next generation of online-information generators, whether you realize it or not, is you. The future of online information dissemination, especially from the perspective of public outreach, but also in terms of student access and exchange among academics, is user-modifiable publishing. Imagine a world in which every publication in an academic discipline was listed online, perhaps in an annotated form, with links to full-text versions? A page that you or anybody else could use. A page that you or anybody else could update, with new publications, or new recipes, or with the addition of an (ideally) improved perspective. Imagine a seamless flow of information, a way of combining all of those many course sites (Bio 101!) that so many of us have worked so hard to develop. Imagine not having to develop ad hoc the technology to make all of this possible. Imagine a place where 10s or more hours of work toward improving the public face of your discipline aren’t destined to be lost at the whims of your department’s computer tech consultant!
All of the technology and great ideas which address many of the problems outlined above are, in principle, solvable. Wikipedia, an online, user-updateable and editable encyclopedia points the way toward the future of less-formal (i.e., other than traditionally published) online scholarship. Technology that is preexisting and easy to use. Unfortunately, its power is damped, enormously, by its strength: Everybody can add information (which, given sufficient volume, can be overwhelming if that information is garbage) and, perhaps more importantly, whole entries can be irretrievably deleted. Nevertheless, I am an optimist and, so far, am of the opinion that these problems, grave as they may be, in fact can be surmounted. Therefore, this essay—and this issue of BEG News— is more about a realistic push for using and contributing to Wikipedia, rather than a call for snubbing it. Thus, I encourage you to visit and contribute to a number of Wikipedia pages that have phage-, phage ecology-, or, more generally, microbial population biology-related themes, which may be found through these Wikipedia “Category” pages:
http://en.wikipedia.org/wiki/Category:Bacteriophage
http://en.wikipedia.org/wiki/Category:Phage_workers
http://en.wikipedia.org/wiki/Category:Microbial_population_biology
Farther down in this issue of BEG News I also present earlier (though slightly updated) copies of some of the pages that may be reached via the above list, ones for which I was either nearly entirely responsible for creating or did in collaboration outside of Wikipedia (and therefore feel reasonably secure in my right to reproduce them):
|
Page presented here |
Wikipedia link |
I place copies of these pages here, in this issue of BEG News, so that you will be able to get a sense of what Wikipedia is all about without having to actually click on a link (or two!) to get there. But please, do go to the Wikipedia versions. In fact, if only for the sake of assuring its survival, if you do nothing else, please go to (and contribute to) this page:
http://en.wikipedia.org/wiki/Phage_meetings
It is crazy that academia has not developed an effective, universal means of disseminating information via the World Wide Web, or maybe we have. Movement is afoot to create a Wikipedia “fork”, called Citizendium (www.citizendium.org), which just may succeed in addressing this lapse while simultaneously subduing Wikipiedia’s more anti-academic tendencies (though, of course, we shall see). Already in existence are a number “private” Wiki-like sites such as those provided by OpenWetWare, where by “private” I mean that these are not open to modification by everybody (that is, of course, not by you). OpenWetWare in particular exists more as a means of within-group communication rather than for the sake of widespread information dissemination to the general public (the latter, of course, is what I and BEG are all about). So please support the phage and phage-ecology presence on Wikipedia—as the best user-modifiable phage web site that we currently have—by using, contributing to, and expanding upon the existing phage and phage ecology entries.
Only you can help create and maintain an effective online phage presence.
Other items found in this issue of BEG News
are a list of new BEG members
and a list of new phage ecology references (with abstracts).
Stephen T. Abedon[1], The Ohio State University
Bacteriophage Ecology Group News (BEG News) 25
The following is my first Wikipedia effort. Feel free to add to the Wikipedia version, found at:
http://en.wikipedia.org/wiki/Phage_ecology.
(equivalent to Wikipedia version as of Saturday, October 21, 2006)
Bacteriophage (phage) are the viruses of bacteria (more generally, of prokaryotes[1]), and phage ecology is the study of the interaction of bacteriophage with their environments.[2]
Contents
Phage "organismal" ecology (suggested reading)
Phage "organismal" experimental protocols (suggested reading)
Phage population ecology (suggested reading)
Phage community ecology (suggested reading)
Phage ecosystem ecology (suggested reading)
Terrestrial phage ecology (suggested reading)
Aquatic phage ecology (suggested reading
Other environments (suggested reading)
Introduction to phage ecology
Vastness of phage ecology
Phage are obligate intracellular parasites meaning that they are able to reproduce only while infecting bacteria. Phage therefore are found only within environments that contain bacteria. Most environments contain bacteria, including our own bodies (there called normal flora). Often these bacteria are found in large numbers[1]. As a consequence, phage are found almost everywhere.
As a rule of thumb, many phage biologists expect that phage population densities will exceed bacterial densities by a ratio of 10-to-1 or more (VBR or virus-to-bacterium ratio; see [2] for a summary of actual data). As there exist estimates of bacterial numbers on Earth of approximately 1030[3], there consequently is an expectation that 1031 or more individual virus (mostly phage[4]) particles exist[5], making phage the most numerous category of "organisms" on our planet.
Bacteria (along with archaeabacteria) appear to be highly diverse and there likely are millions of species[6]. Phage-ecological interactions therefore are quantitatively vast: huge numbers of intereactions. Phage-ecological interations are also qualitatively diverse: There are huge numbers of environment types, bacterial-host types[7], and also individual phage types[8]).
Studying phage ecology
The scale of phage ecology is at once both exhilarating and intimidating. As a guiding principle toward understanding phage ecology we therefore seek generalizations, plus look to more established scientific disciplines for guidance, the most obvious being general ecology. Toward that end we can speak of phage "organismal" ecology, population ecology, community ecology, and ecosystem ecology. Phage ecology from these perspectives will be described in turn (re: links in previous sentence).
Phage ecology also may be considered (though mostly less well formally explored) from perspectives of phage behavioral ecology, evolutionary ecology, functional ecology, landscape ecology, mathematical ecology, molecular ecology, physiological ecology (or ecophysiology), and spatial ecology. Phage ecology additionally draws (extensively) from microbiology, particularly in terms of environmental microbiology, but also from an enormous catalog (90 years) of study of phage and phage-bacterial interactions in terms of their physiology and, especially, their molecular biology.
Suggestions for further reading are provided below.
Phage "organismal" ecology
Phage "organismal" ecology is primarily the study of the evolutionary ecological impact of phage growth parameters:
latent period, plus
eclipse period (or simply "eclipse")
rise period (or simply "rise")
burst size, plus
rate of intracellular phage-progeny maturation
adsorption constant, plus
rates of virion diffusion
virion decay (inactivation) rates
host range, plus
resistance to restriction
resistance to abortive infection
various temperate-phage properties, including
rates of reduction to lysogeny
rates of lysogen induction
the tendency of at least some phage to enter into (and then subsequently leave) a not very well understood state known (inconsistently) as pseudolysogeny
Another way of envisioning phage "organismal" ecology is that it is the study of phage adaptations that contribute to phage survival and transmission to new hosts or environments. Phage "organismal" ecology is the most closely aligned of phage ecology disciplines with the classical molecular and molecular genetic analyses of bacteriophage.
From the perspective of ecological subdisciplines, we can also consider phage behavioral ecology, functional ecology, and physiological ecology under the heading of phage "organismal" ecology. However, as noted, these subdisciplines are not as well developed as more general considerations of phage "organismal" ecology. Phage growth parameters often evolve over the course of phage experimental adaptation studies.
Suggestions for further reading are provided below.
Historical overview
In the mid 1910s, when phage were first discovered, the concept of phage was very much a whole-culture phenomenon (like much of microbiology[3]), where various types of bacterial cultures (on solid media, in broth) were visibly cleared by phage action. Though from the start there was some sense, especially by Fėlix d'Hėrelle, that phage consisted of individual "organisms", in fact it wasn't until the late 1930s through the 1940s that phage were studied, with rigor, as individuals, e.g., by electron microscopy and single-step growth experiments (example of latter). Note, though, that for practical reasons much of "organismal" phage study is of their properties in bulk culture (many phage) rather than the properties of individual phage virions or or individual infections.
This somewhat whole-organismal view of phage biology saw its heyday during the 1940s and 1950s, before giving way to much more biochemical, molecular genetic, and molecular biological analyses of phage, as seen during the 1960s and onward. This shift, paralleled in much of the rest of microbiology[9], represented a retreat from a much more ecological view of phages (first as bacterial killers, and then as organisms unto themselves). However, the organismal view of phage biology lives on as a foundation of phage ecological understanding. Indeed, it represents a key thread that ties together the ecological thinking on phage ecology with the more "modern" considerations of phage as molecular model systems.
Methods
The basic experimental toolkit of phage "organismal" ecology consists of the single-step growth (or one-step growth; example) experiment and the phage adsorption curve (example). Single-step growth is a means of determining the phage latent period (example), which is approximately equivalent (depending on how it is defined) to the phage period of infection. Single-step growth experiments also are employed to determine a phage's burst size, which is the number of phage (on average) that are produced per phage-infected bacterium.
The adsorption curve is obtained by measuring the rate at which phage virion particles (see [10]) attach to bacteria. This is usually done by separating free phage from phage-infected bacteria in some manner so that either the loss of not currently infecting (free) phage or the gain of infected bacteria may be measured over time.
Suggestions for further reading are provided below.
Phage population ecology
A population is a group of individuals which either do or can interbreed or, if incapable of interbreeding, then are recently derived from a single individual (a clonal population). Population ecology considers characteristics that are apparent in populations of individuals but either are not apparent or are much less apparent among individuals. These characteristics include so-called intraspecific interactions, that is between individuals making up the same population, and can include competition as well as cooperation. Competition can be either in terms of rates of population growth (as seen especially at lower population densities in resource-rich environments) or in terms of retention of population sizes (seen especially at higher population densities where individuals are directly competing over limited resources). Respectively, these are population-density independent and dependent effects.
Phage population ecology considers issues of rates of phage population growth, but also phage-phage interactions as can occur when two or more phage adsorb an individual bacterium.
Suggestions for further reading are provided below.
Phage community ecology
A community consists of all of the biological individuals found within a given environment (more formally, within an ecosystem), particularly when more than one species is present. Community ecology studies those characteristics of communities that either are not apparent or which are much less apparent if a community consists of only a single population. Community ecology thus deals with interspecific interactions. Interspecific interactions, like intraspecific interactions, can range from cooperative to competitive but also to quite antagonistic (as are seen, for example, with predator-prey interactions). An important consequence of these interactions is coevolution.
The interaction of phage with bacteria is the primary concern of phage community ecologists. Phage, however, are capable of interacting with species other than bacteria, e.g., such as phage-encoded exotoxin interaction with animals[11]. Phage therapy is an example of applied phage community ecology.
Suggestions for further reading are provided below.
Phage ecosystem ecology
An ecosystem consists of both the biotic and abiotic components of an environment. Abiotic entities are not alive and so an ecosystem essentially is a community combined with the non-living environment within which that ecosystem exists. Ecosystem ecology naturally differs from community ecology in terms of the impact of the community on these abiotic entities, and vice versa. In practice, the portion of the abiotic environment of most concern to ecosystem ecologists is inorganic nutrients and energy.
Phage impact the movement of nutrients and energy within ecosystems primarily by lysing bacteria. Phage can also impact abiotic factors via the encoding of exotoxins (a subset of which are capable of solubilizing the biological tissues of living animals[12]). Phage ecosystem ecologists are primarily concerned with the phage impact on the global carbon cycle, especially within the context of a phenomenon know as the microbial loop.
Suggestions for further reading are provided below.
External links
Further reading
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[4]. 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 0-195-14850-9
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 1-555-81307-0
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 0-849-31336-8
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 0-123-62675-7
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 0-125-93690-7
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 0-849-36056-0
Ackermann, H.-W., and M. S. DuBow. 1987. Viruses of Prokaryotes, Volume 2, Natural Groups of Bacteriophages. CRC Press, Boca Raton, Florida. ISBN 0-849-36056-0
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 0-195-14850-9
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 1-555-81307-0
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 0-849-31336-8
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 0-123-62675-7
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 1-555-81196-5
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 1-555-81064-0
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 0-849-31336-8
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 1-555-81064-0
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 1-555-81064-0
Carlson, K. 1994. Single-step growth, p. 434-437. In J. D. Karam (ed.), Molecular Biology of Bacteriophage T4. ASM Press, Washington. ISBN 1-555-81064-0
Snustad, D. P., and D. S. Dean. 1971. Genetics Experiments with Bacterial Viruses. W. H. Freeman and Co., San Francisco. ISBN 0-716-70161-8
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 0-195-14850-9
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 0-195-14850-9
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 0080420001
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 0-125-93690-7
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 0-878-93229-1
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 0-792-34735-8
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 0-123-62675-7
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 0-125-28620-1
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 0-849-31336-8
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,