Phage ecology
Encyclopedia
Bacteriophage
s (phages), potentially the most numerous "organisms" on Earth, are the viruses of bacteria
(more generally, of prokaryotes
provides a history.). Phage ecology is the study of the interaction of bacteriophage
s with their environments
. Phage ecology is increasingly an important component of sessions and symposiums associated with phage meetings as well as general microbiological meetings.
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 http://www.phage.org/bgnws007.htm#submissions, making phages the most numerous category of "organisms" on our planet.
Bacteria (along with archaeabacteria) 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).
. Accordingly, phage ecology is treated under the following heads "organismal" ecology, population ecology, community ecology, and ecosystem ecology. 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
.
impact of phage growth parameters:
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.
, 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. 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.
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 http://mmbr.asm.org/cgi/content/full/68/2/173#The_Dismantling_of_Bacteriology_and_a_Deconstruction_of_the_Procaryote, 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
.
, 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 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.
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 size
s (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.
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 animalshttp://www.la-press.com/evolbio05.htm. Phage therapy
is an example of applied phage community ecology.
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 tissue
s of living animalshttp://www.la-press.com/evolbio05.htm). 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
.
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
s (phages), potentially the most numerous "organisms" on Earth, are the viruses of bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
(more generally, of prokaryotes
provides a history.). Phage ecology is the study of the interaction of bacteriophage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
s with their environments
Natural environment
The natural environment encompasses all living and non-living things occurring naturally on Earth or some region thereof. It is an environment that encompasses the interaction of all living species....
. Phage ecology is increasingly an important component of sessions and symposiums associated with phage meetings as well as general microbiological meetings.
Vastness of phage ecology
Phages are obligate intracellular parasites meaning that they are able to reproduce only while infecting bacteria. Phages therefore are found only within environments that contain bacteria. Most environments contain bacteria, including our own bodies (called normal flora). Often these bacteria are found in large numbers. As a consequence, phages are found almost everywhere.As a rule of thumb
Rule of thumb
A rule of thumb is a principle with broad application that is not intended to be strictly accurate or reliable for every situation. It is an easily learned and easily applied procedure for approximately calculating or recalling some value, or for making some determination...
, 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 http://www.phage.org/bgnws007.htm#submissions, making phages the most numerous category of "organisms" on our planet.
Bacteria (along with archaeabacteria) 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).
Studying phage ecology
The study of phage ecology reflects established scientific disciplines in ecological studies in scope, the most obvious being general ecologyEcology
Ecology is the scientific study of the relations that living organisms have with respect to each other and their natural environment. Variables of interest to ecologists include the composition, distribution, amount , number, and changing states of organisms within and among ecosystems...
. Accordingly, phage ecology is treated under the following heads "organismal" ecology, population ecology, community ecology, and ecosystem ecology. Phage ecology also may be considered (though mostly less well formally explored) from perspectives of phage behavioral ecology
Behavioral ecology
Behavioral ecology, or ethoecology, is the study of the ecological and evolutionary basis for animal behavior, and the roles of behavior in enabling an animal to adapt to its environment...
, evolutionary ecology
Evolutionary ecology
Evolutionary ecology lies at the intersection of ecology and evolutionary biology. It approaches the study of ecology in a way that explicitly considers the evolutionary histories of species and the interactions between them. Conversely, it can be seen as an approach to the study of evolution that...
, functional ecology
Functional ecology
Functional ecology is the branch of ecology that focuses on the roles, or functions, that species play in the community or ecosystem in which they occur. In this approach, physiological, anatomical, and life history characteristics of the species are emphasized...
, landscape ecology
Landscape ecology
Landscape ecology is the science of studying and improving relationships between urban development and ecological processes in the environment and particular ecosystems...
, mathematical ecology, molecular ecology
Molecular ecology
Molecular ecology is a field of evolutionary biology that is concerned with applying molecular population genetics, molecular phylogenetics, and more recently genomics to traditional ecological questions...
, physiological ecology (or ecophysiology), and spatial ecology
Spatial ecology
Spatial ecology is a specialization of ecologyand geography that is concerned with the identification of spatial patterns and their relationships to ecological events. In spatial ecology, ecological events can be explained through the detection of patterns at a given spatial scale; local,...
. Phage ecology additionally draws (extensively) from microbiology
Microbiology
Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
, 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
Physiology
Physiology is the science of the function of living systems. This includes how organisms, organ systems, organs, cells, and bio-molecules carry out the chemical or physical functions that exist in a living system. The highest honor awarded in physiology is the Nobel Prize in Physiology or...
and, especially, their molecular biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
.
Phage "organismal" ecology
Phage "organismal" ecology is primarily the study of the evolutionary ecologicalEvolutionary ecology
Evolutionary ecology lies at the intersection of ecology and evolutionary biology. It approaches the study of ecology in a way that explicitly considers the evolutionary histories of species and the interactions between them. Conversely, it can be seen as an approach to the study of evolution that...
impact of phage growth parameters:
- latent period, plus
- eclipse period (or simply "eclipse")
- rise period (or simply "rise")
- burst sizeFecundityFecundity, derived from the word fecund, generally refers to the ability to reproduce. In demography, fecundity is the potential reproductive capacity of an individual or population. In biology, the definition is more equivalent to fertility, or the actual reproductive rate of an organism or...
, 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 lysogenyLysogenyLysogeny, or the lysogenic cycle, is one of two methods of viral reproduction . Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome...
- rates of lysogen induction
- rates of reduction to lysogeny
- 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
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
and molecular genetic
Molecular genetics
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology...
analyses of bacteriophage.
From the perspective of ecological subdisciplines
Ecology
Ecology is the scientific study of the relations that living organisms have with respect to each other and their natural environment. Variables of interest to ecologists include the composition, distribution, amount , number, and changing states of organisms within and among ecosystems...
, we can also consider phage behavioral ecology
Behavioral ecology
Behavioral ecology, or ethoecology, is the study of the ecological and evolutionary basis for animal behavior, and the roles of behavior in enabling an animal to adapt to its environment...
, functional ecology
Functional ecology
Functional ecology is the branch of ecology that focuses on the roles, or functions, that species play in the community or ecosystem in which they occur. In this approach, physiological, anatomical, and life history characteristics of the species are emphasized...
, 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), where various types of bacterial cultures (on solid mediaAgar plate
An agar plate is a Petri dish that contains a growth medium used to culture microorganisms or small plants like the moss Physcomitrella patens.Selective growth compounds may also be added to the media, such as antibiotics....
, in broth
Broth
Broth is a liquid food preparation, typically consisting of either water or an already flavored stock, in which bones, meat, fish, cereal grains, or vegetables have been simmered. Broth is used as a basis for other edible liquids such as soup, gravy, or sauce. It can be eaten alone or with garnish...
) 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. 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.
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
Molecular genetics
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology...
, and molecular biological
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
analyses of phage, as seen during the 1960s and onward. This shift, paralleled in much of the rest of microbiology http://mmbr.asm.org/cgi/content/full/68/2/173#The_Dismantling_of_Bacteriology_and_a_Deconstruction_of_the_Procaryote, 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
Molecular modelling
Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
.
Methods
The basic experimental toolkit of phage "organismal" ecology consists of the single-step growth (or one-step growth;) experiment and the phage adsorption curve. 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 sizeFecundity
Fecundity, derived from the word fecund, generally refers to the ability to reproduce. In demography, fecundity is the potential reproductive capacity of an individual or population. In biology, the definition is more equivalent to fertility, or the actual reproductive rate of an organism or...
, 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 Virion#Structure) attach to bacteria. This is usually done by separating free phage from phage-infected bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
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 populationPopulation
A population is all the organisms that both belong to the same group or species and live in the same geographical area. The area that is used to define a sexual population is such that inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals...
is a group of individuals which either do or can interbreed
Sexual reproduction
Sexual reproduction is the creation of a new organism by combining the genetic material of two organisms. There are two main processes during sexual reproduction; they are: meiosis, involving the halving of the number of chromosomes; and fertilization, involving the fusion of two gametes and the...
or, if incapable of interbreeding, then are recently derived from a single individual (a clonal population
Clonal colony
A clonal colony or genet is a group of genetically identical individuals that have grown in a given location, all originating vegetatively from a single ancestor. In plants, an individual in such a population is referred to as a ramet...
). Population ecology
Population ecology
Population ecology is a sub-field of ecology that deals with the dynamics of species populations and how these populations interact with the environment. It is the study of how the population sizes of species living together in groups change over time and space....
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
Intraspecific competition
Intraspecific competition is a particular form of competition in which members of the same species vie for the same resource in an ecosystem...
as well as cooperation
Cooperation
Cooperation or co-operation is the process of working or acting together. In its simplest form it involves things working in harmony, side by side, while in its more complicated forms, it can involve something as complex as the inner workings of a human being or even the social patterns of a...
. Competition can be either in terms of rates of population growth
Population growth
Population growth is the change in a population over time, and can be quantified as the change in the number of individuals of any species in a population using "per unit time" for measurement....
(as seen especially at lower population densities in resource-rich environments) or in terms of retention of population size
Population size
In population genetics and population ecology, population size is the number of individual organisms in a population.The effective population size is defined as "the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under...
s (seen especially at higher population densities where individuals are directly competing over limited resources). Respectively, these are population-density
Population density
Population density is a measurement of population per unit area or unit volume. It is frequently applied to living organisms, and particularly to humans...
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 communityCommunity
The term community has two distinct meanings:*a group of interacting people, possibly living in close proximity, and often refers to a group that shares some common values, and is attributed with social cohesion within a shared geographical location, generally in social units larger than a household...
consists of all of the biological individuals found within a given environment (more formally, within an ecosystem
Ecosystem
An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....
), particularly when more than one species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
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
Population
A population is all the organisms that both belong to the same group or species and live in the same geographical area. The area that is used to define a sexual population is such that inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals...
. 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
Exotoxin
An exotoxin is a toxin excreted by a microorganism, like bacteria, fungi, algae, and protozoa. An exotoxin can cause damage to the host by destroying cells or disrupting normal cellular metabolism. They are highly potent and can cause major damage to the host...
interaction with animalshttp://www.la-press.com/evolbio05.htm. Phage therapy
Phage therapy
Phage therapy is the therapeutic use of bacteriophages to treat pathogenic bacterial infections. Although extensively used and developed mainly in former Soviet Union countries circa 1920, this method of therapy is still being tested for treatment of a variety of bacterial and poly-microbial...
is an example of applied phage community ecology.
Phage ecosystem ecology
An ecosystemEcosystem
An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....
consists of both the biotic
Biotic component
Biotic components are the living things that shape an ecosystem. A biotic factor is any living component that affects another organism, including animals that consume the organism in question, and the living food that the organism consumes. Each biotic factor needs energy to do work and food for...
and abiotic components of an environment. Abiotic entities are not alive and so an ecosystem essentially is a community
Community
The term community has two distinct meanings:*a group of interacting people, possibly living in close proximity, and often refers to a group that shares some common values, and is attributed with social cohesion within a shared geographical location, generally in social units larger than a household...
combined with the non-living environment within which that ecosystem exists. Ecosystem ecology
Ecosystem ecology
Ecosystem ecology is the integrated study of biotic and abiotic components of ecosystems and their interactions within an ecosystem framework. This science examines how ecosystems work and relates this to their components such as chemicals, bedrock, soil, plants, and animals.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
Energy
In physics, energy is an indirectly observed quantity. It is often understood as the ability a physical system has to do work on other physical systems...
.
Phage impact the movement of nutrients and energy within ecosystems primarily by lysing
Lysis
Lysis refers to the breaking down of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a "lysate"....
bacteria. Phage can also impact abiotic factors via the encoding of exotoxins (a subset of which are capable of solubilizing the biological tissue
Biological tissue
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...
s of living animalshttp://www.la-press.com/evolbio05.htm). Phage ecosystem ecologists are primarily concerned with the phage impact on the global carbon cycle
Carbon cycle
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth...
, especially within the context of a phenomenon known as the microbial loop
Microbial loop
The microbial loop describes a trophic pathway in the marine microbial food web where dissolved organic carbon is returned to higher trophic levels via the incorporation into bacterial biomass, and coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. The term microbial...
.
External links
- The Bacteriophage Ecology Group (BEG): Home of Phage Ecology and Phage Evolutionary Biology (www.phage.org)
- The Virus Ecology Group (VEG)
- An online, searchable phage ecology bibliography can be found here (>6000 references).
- An interactive model for an evolving ecology of phages and bacteria.