Phage ecology

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prokaryotes[1]). Phage ecology is the study of the interaction of bacteriophages with their environments.[2]

Introduction to phage ecology

Vastness of phage ecology

Phages are

normal flora). Often these bacteria are found in large numbers. As a consequence, phages are found almost everywhere.[citation needed
]

As a

organisms
" on our planet.

Bacteria (along with archaea) appear to be highly diverse and there possibly are millions of species.[6] 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,[7] and also individual phage types[8]

Studying phage ecology

The study of phage ecology reflects established scientific disciplines in ecological studies in scope, the most obvious being general

phage and phage-bacterial interactions in terms of their physiology and, especially, their molecular biology.[citation needed
]

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
  • the tendency of at least some phage to enter into (and then subsequently leave) a not very well understood state known (inconsistently) as pseudolysogeny[9][10]

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

electron microscopy and single-step growth experiments.[12] 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 individual infections.[citation needed
]

This somewhat whole-organismal view of phage biology saw its heyday during the 1940s and 1950s, before giving way to much more

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.[citation needed
]

Methods

The basic experimental toolkit of phage "organismal" ecology consists of the single-step growth (or one-step growth;[12]) experiment and the phage adsorption curve.[13] 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.[citation needed]

The adsorption curve is obtained by measuring the rate at which phage

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.[citation needed
]

Phage population ecology

A

limited resources). Respectively, these are population-density independent and dependent effects.[citation needed
]

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

predator-prey interactions). An important consequence of these interactions is coevolution
.

Relationship with bacteria

The interaction of phage with

Bacterial resistance to phages puts pressure on the phages to develop stronger effects on the bacteria. The Red Queen hypothesis describes this relationship, as the organisms must constantly adapt and evolve in order to survive.[15]
This relationship is important to understand as phages are now being used for more practical and medicinal purposes.

Bacteria have developed multiple defense mechanisms to fight off the effects of bacteriophages.

methylase.[16] 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.[18] 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.[16]
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 abortive 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.[16]

On top of the above mentioned strategies, a growing arsenal of anti-phage immune systems has been described and quantified in bacteria.[19]

Phages are also capable of interacting with species other than bacteria, e.g., such as phage-encoded

animals.[20] Phage therapy is an example of applied phage community ecology.[citation needed
]

Phage ecosystem ecology

An

nutrients and energy
.

Phages impact the movement of nutrients and energy within ecosystems primarily by

animals [3]). 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
.

Notes

  1. PMID 15187180. The Dismantling of Bacteriology and a Deconstruction of the Procaryote {{cite journal}}: External link in |quote= (help
    ); see also pp. 103–4 of Sapp, Jan (2004). "Evolving biological organization". Microbial phylogeny and evolution: concepts and controversies. Oxford [Oxfordshire]: Oxford University Press. pp. 99–118.
    ISBN 978-0-19-516877-8
    .
    Sapp J (September 2006).     "Two faces of the prokaryote concept" (PDF). Int. Microbiol. 9 (3): 163–72.
    PMID 17061206
    . provides a history.
  2. ^ 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.
  3. PMID 15109783
    .
  4. PMID 9618454
    .
  5. PMID 10704475
    .
  6. PMID 12097644
    .
  7. PMID 16880384
    .
  8. PMID 12384570
    .
  9. PMID 4215366
    .
  10. ISBN 978-0-12-680126-2
    .
  11. S2CID 36544748
    .
  12. ^
    PMID 11889095
    .
  13. PMID 14660403
    .
  14. PMID 20979102
    .
  15. S2CID 82562085
    .
  16. ^
    ISSN 0265-9247
    issue v33i0001 article 43
  17. PMID 12028776
    .
  18. ISSN 0092-8240
    issue v62i0004 article 759
  19. PMC 10924106
    .
  20. ^ "Evolutionary Bioinformatics Online 2005". Libertas Academica. Archived from the original on 2006-05-26.

External links

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