Phage ecology
Bacteriophage (phage) are parasites of bacteria. Potentially the most numerous "organisms" on Earth, these viruses infect prokaryotes[1]). Phage ecology is the study of the interaction of bacteriophage with their environments.[2]
Introduction to phage ecology
Vastness of phage ecology
Since phage are obligate intracellular parasites, they are able to reproduce only while infecting bacteria and therefore "live" in a bacterial habitat. Since they are viruses, the world live was put in quotation marks. Phage particles take over the cellular machinery of living things in order to reproduce, whether they (or any virus) is properly called alive is a matter of some debate. AIn any event, phage are restricted to environments that contain bacteria, but this leaves them a broad range of habitats, including our own bodies. In our bodies, phage are known to infect both the bacteria that colonize our tissues (called normal flora), and those bacteria that infect us and cause disease (called pathogens. When phage particles are found in bacteria they are ordinarily found in multiple copies, and when bacteria are found in any habitat they are ordinarily present in large numbers. 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 [1] for a summary of actual data). As there exist estimates of bacterial numbers on Earth of approximately 1030[2], there consequently is an expectation that 1031 or more individual virus (mostly phage[3]) particles exist[4], 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[5]. Phage-ecological interactions therefore are quantitatively vast: huge numbers of interactions. Phage-ecological interactions are also qualitatively diverse: There are huge numbers of environment types, bacterial-host types[6], and also individual phage types[7]).
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.
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[3]
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.
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[4]), 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[8], 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 attach to bacteria.[5] 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.
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.
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[9]. Phage therapy is an example of applied phage community ecology.
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[10]). 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.
An interactive and highly simplified model for an evolving ecology of phages and bacteria can be found on Cmol.
Notes
- ↑ The term "prokaryotes" is useful to mean the sum of the bacteria and archaeabacteria but otherwise can be controversial, as discussed by Woese, 2004; see also pp. 103-104 of Woese, C. R. 2005. Evolving biological organization, p. 99-118. In J. Sapp (ed.), Microbial Phylogeny and Evolution Concepts and Controversies. Oxford University Press, Oxford.
- ↑ This article on phage ecology was expanded from a stub during the writing of the first chapter of the edited monograph, Bacteriophage Ecology (forecasted publication date: 2007, Cambridge University Press), in order to be cited by that chapter especially as a repository of phage ecology review chapters and articles.
- ↑ Pseudolysogeny references: Barksdale, L., and S. B. Ardon. 1974. Persisting bacteriophage infections, lysogeny, and phage conversions. Ann. Rev. Microbiol. 28:265-299; Miller, R. V., and S. A. Ripp. 2002. Pseudolysogeny: A bacteriophage strategy for increasing longevity in situ, p. 81-91. In M. Syvanen and C. I. Kado (eds.), Horizontal Gene Transfer. Academic Press, San Diego.
- ↑ Summers, W. C. 1991. From culture as organisms to organisms as cell: historical origins of bacterial genetics. J. Hist. Biol. 24:171-190.
- ↑ Yongping, Shao; Ing-Nang Wang (2008 September). "Bacteriophage Adsorption Rate and Optimal Lysis Time". Genetics 180 (1): 471–482. DOI:10.1534/genetics.108.090100. PMC2535697. Retrieved on 25 October 2013. Research Blogging.