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(bacteriophages), potentially the most numerous "organisms" on Earth, are the viruses of bacteria (more generally, of prokaryotesThe term "prokaryotes" is useful to mean the sum of the bacteria and archaea but otherwise can be controversial, as discussed by ; see also pp. 103–4 of
provides a history.
). '''Phage ecology''' is the study of the interaction of [[bacteriophage]]s with their environments.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: March, 2008, Cambridge University Press), in order to be cited by that chapter especially as a repository of phage ecology review chapters and articles.
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 for a summary of actual data). As there exist estimates of bacterial numbers on Earth of approximately 1030, there consequently is an expectation that 1031 or more individual virus (mostly phage) particles exist [1], making phages the most numerous category of "organisms" on our planet.
Bacteria (along with archaea) appear to be highly diverse and there possibly are millions of species. 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, and also individual phage types
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 Ecology, 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.
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 phages, as seen during the 1960s and onward. This shift, paralleled in much of the rest of microbiology [2], 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.
The adsorption curve is obtained by measuring the rate at which phage virion particles (see Virion#Structure) 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.
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.
Bacteria have developed multiple defense mechanisms to fight off the effects of bacteriophages. issue v33i0001 article 43 In experimentation, amount of resistance can be determined by how much of a plate (generally agar with bacteria, infected with phages) ends up being clear. The clearer, the less resistant as more bacteria have been lysed. The most common of these defense mechanisms is called the restriction-modification system (RM system). In this system, foreign DNA trying to enter the bacterial host is restricted by endonucleases that recognize specific base pairs within the DNA, while the DNA of the cell is protected from restriction due to methylase. RM systems have evolved to keep up with the ever-changing bacteria and phage. In general, these RM types differ in the nucleotide sequences that they recognize. issue v62i0004 article 759 However, there is an occasional slip where the endonuclease misses the DNA sequence of the phage and the phage DNA is able to enter the cell anyway, becoming methylated and protected against the endonuclease. This accident is what can spur the evolution of the RM system. Phages can acquire or use the enzyme from the host cell to protect their own DNA, or sometimes they will have proteins that dismantle the enzyme that is meant to restrict the phage DNA. Another option is for the phage to insert different base pairs into its DNA, thereby confusing the enzyme.
Another mechanism employed by bacteria is referred to as CRISPR. This stands for “clustered regularly interspersed palindromic repeats” which means that the immunity to phages by bacteria has been acquired via adding spacers of DNA that are identical to that of the DNA from the phage. Some phages have been found to be immune to this mechanism as well. In some way or another, the phages have managed to get rid of the sequence that would be replicated.
A third way that bacteria have managed to escape the effects of bacteriophages is by infection. This is a last resort option- when the host cell has already been infected by the phage. This method is not ideal for the host cell, as it still leads to its death. The redeeming feature of this mechanism is the fact that it interferes with the phage processes and prevents it from then moving on to infect other cells.
On top of the above mentioned strategies, a growing arsenal of anti-phage immune systems has been described and quantified in bacteria.
Phages are also capable of interacting with species other than bacteria, e.g., such as phage-encoded exotoxin interaction with animals. Phage therapy is an example of applied phage community ecology.
Phages impact the movement of nutrients and energy within ecosystems primarily by Lysis bacteria. Phages can also impact abiotic factors via the encoding of exotoxins (a subset of which are capable of solubilizing the biological tissues of living animals [4]). Phage ecosystem ecologists are primarily concerned with the phage impact on the global carbon cycle, especially within the context of a phenomenon known as the microbial loop.
Phage ecosystem ecology
An ecosystem consists of both the Biotic component 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.
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