Two additional concepts of natural selection are important to mention under the guise of microbial evolution. These are frequency-dependent selection along with inclusive fitness. Frequency-dependent selection is one answer to the question of how natural selection can stably maintain two or more alleles at a given locus within a population (balanced polymorphism) while inclusive fitness helps to explain how the evolution of cooperation among organisms and perhaps particularly among microorganisms can be possible.
A simplistic view of selection is that it will tend to increase the frequency of beneficial alleles while at the same time decrease the frequency of detrimental alleles. One complication on this view is that the fitness associated with an allele is a function of not only the allele's genetic background (the overall genotype) but also the environment within which the organism carrying the allele exists. A further complication is that the characteristics of an environment can be influenced by both what alleles exist in that environment and those allele's frequency or density. Thus, the fitness associated with a given allele can change as a function of the frequency of that allele. The result is a phenomenon known as frequency-dependent selection.
There exist two types of frequency-dependent selection, that where an allele's fitness increases as a function of its density (i.e., allele fitness increases as a function of allele frequency) and that were an allele's fitness decreases as its frequency increases. One can view the former, so-called disruptive frequency-dependent selection, as an example, on evolutionary time scales, of positive feedback, that is, further increase in a signal in response to increases in that signal. One non-biological example of positive feedback is the "audio feedback" experienced in rock music where the sound from speakers is acquired from the "pickups" that normally record the vibrations emanating from the guitar strings, which is then amplified prior to being broadcast from the same speakers, and so on. An important biological example is the hormonal positive feedback that occurs within a pregnant mammal that ultimately results in birth of a baby, i.e., oxytocin is released in response to pressure on the cervix which leads to uterine contractions and greater pressure on the cervix and so on. These though are examples of positive feedback rather than of disruptive frequency-dependent selection.
In microbial systems, disruptive frequency-dependent selection is typically associated with production of antagonistic factors such are bacteriocins or antibiotics, where high densities of factors are necessary to effect negative impacts on susceptible organisms, such as conspecifics. What that means is that allele fitness and frequencies will tend to be relatively low until circumstances result in higher frequencies, at which point organism and therefore factor densities may be high enough to eliminate competing alleles. Note though that these high frequencies can exist extremely locally, and thus spatial structure can result such positive feedbacks. This is an example of soft selection, i.e., an increase in the competitive ability of an organism – such as when considering bacteriocins that tend to affect only conspecifics – rather increasing than the overall fitness of a population.
The other form of frequency-dependent selection, by contrast, can be described as stabilizing. Stabilizing frequency-dependent selection is analogous to negative feedback, that is, the fitness of an allele declines as its frequency increases. This may be illustrated in terms of the thermostat in a building or cruise control in a vehicle. The former is linked with a furnace and as temperatures increase in the vicinity of the thermostat, an inhibiting signal is sent to the furnace, turning it down or off. Alternatively, when temperatures decline in the vicinity of the thermostat, a signal is sent to the furnace to turn it on (or up). The result is a more stable temperature than one could achieve manually. Similarly, a cruise control on an automobile detects velocity and increases engine output in response to reduced speeds or decreases engine output in response to increased speeds. Homeostasis, as observed within multicellular organisms, can be viewed as a series of negative feedback loops that have the effect of stabilizing characteristics internal to bodies. With stabilizing frequency dependent selection, thus reduction in allele frequencies results in selection for increases in their frequencies whereas increases are countered by selection against those same alleles.
Stabilizing frequency-dependent selection is typically seen in association with predator-prey type community interactions. The basic idea is that predators are not infinitely versatile but instead will behaviorally, morphologically, or physiologically specialize on specific prey types. Specialization, all else held constant, will tend to be toward more common prey types. As a consequence, less common prey types may experience fitness benefits. That is, rarer alleles can be more beneficial. An example of this process is seen with the phenomenon dubbed "Kill the winner" where more successful phage-susceptibility types of bacteria will be more susceptible to phage attack than less successful types simply because more-successful bacteria will tend to be more prevalent and therefore able to support phage population growth to higher, more potentially bacteria-eradicating densities. Note that the strength of frequency-dependent selection, in this scenario, will be a direct function of predator prevalence, that is, it is predator action that constitutes the selective force.
Note, by the way, the equivalence between stabilizing frequency-dependent selection and simply diversifying selection. This can be confusing, however, since diversifying selection often is contrasted with stabilizing selection. The reason for the seeming confusing is that with stabilizing selection what is being "stabilized" is a single trait whereas with stabilizing frequency-dependent selection what is being stabilized is a polymorphism. Stabilizing frequency-dependent selection thus is similar to diversifying selection, since both give rise to the maintenance of multiple alleles at a single locus. Disruptive frequency-dependent selection, by contrast, is similar in its outcome to stabilizing selection, again because what is being disrupted is a polymorphism, while what is being stabilized with stabilizing selection in essence is the absence of a polymorphism.
Interestingly, predator-prey interactions can also give rise to a form of disruptive frequency-dependent selection. In this case, protective measures displayed by prey organisms can give rise to a frequency-dependent selection in which predator organisms learn (behaviorally or perhaps also evolutionarily) to come to avoid unpleasant prey types (essentially a behavior on the part of the predator that is an opposite of specialization). The result can be a mimicry among potential prey such that the characteristics recognized by the predator organisms, which predators associate with poor prey, are acquired by other prey types. That is, once a characteristic indicating "bad prey" to predators becomes sufficiently common, the fitness associated with displaying those characteristics becomes greater. The less complicated form of this mimicry, where "bad prey" come to resemble each other is known as Müllerian mimicry. Alternatively, it is possible for "good prey" to take on these same characteristics (i.e., other than the bad character itself), a process known as Batesian mimicry, which can be viewed as a form of disruptive frequency-dependent selection. Thus, if "good prey" should increase sufficiently in density relative to "bad prey" then the fitness benefit of the "bad prey" signal to predators will be reduced. I am unaware of either mimicry form explicitly operating within microbial systems, however.
Natural selection was initially understood as well as most readily comprehended in terms of its action on individual organisms. The concept of Darwinian fitness, however, is commonly defined into terms of individual genes/alleles/loci. It should come as no surprise, therefore, that natural selection can easily be conceptualized in terms other than the fitness of individual organisms but instead in terms of its action on individual genes. This perspective leads easily into three concepts that are relevant to an understanding of more sophisticated aspects of evolutionary biology including inclusive fitness, kin selection, and the idea of multilevel selection. Each of these has at its basis variation in what is considered to be the unit of selection, that is, upon which natural selection acts. Relevant too is Richard Dawkin’s the concept of selfish genes.
Humans are probably hardwired towards viewing individual organisms, such as ourselves, as inherently important biological concepts. We might occasionally be confused about what exactly is an individual organism, versus especially groups of individual organisms, but nonetheless our tendency in viewing our biotic environment is to reduce our perspective to the properties of individuals: Individual trees, individual dogs, individual friends, etc. From that perspective we can then consider parts of individuals, on the one hand, e.g., arms, legs, cells, and groups of individuals on the other.
From the perspective of evolutionary biology, the individual also is fundamentally and inherently important. It is in particular individuals that reproduce, and individuals that either do or don't survive to reproduce, and it is individuals that are generated in the process of reproduction. Individual genes also can be copied, in the course of reproduction, and to varying degrees can be passed around between individuals in manner that is somewhat independent of the reproduction of individual organisms. Thus, and importantly, genes often can be shared among individuals. The result is that individual genes can serve as units of selection. In a manner, the reproduction of genes, that is, can under certain circumstances take preference, in terms of natural selection, even over the reproduction of individuals that carry those genes.
The primary means by which this concept of gene fitness takes some precedence over the fitness of individual organisms is seen, again, in the concepts of inclusive fitness, kin selection, and also that of the selfish gene. Interestingly, though in all of these cases the genes or alleles involved can be viewed as being selfish relative to their carrier organisms, it is in fact such selfishness that actually is thought to give rise to many instances of cooperation between individual organisms. Thus, gene selfishness can lead directly to a lack of selfishness among the carriers of those genes: A gene can be selfish in forcing its carrier to be not selfish!
A bit of Richard Dawkins on his subject of selfish gene:
Inclusive fitness literally means inclusion of the fitness of multiple individuals in determining an allele's Darwinian fitness. The result is that it is average fitness among these individuals that determines actual fitness (noting, as an aside, that even here the fitness of individual organisms is important). Thus, it is possible for fitness to vary between the individuals carrying a specific allele and indeed that is key to the importance of inclusive fitness, with some individuals displaying very low fitness (e.g., they die without reproducing) while others display relatively high fitnesses. Indeed, given inclusive fitness it is relatively easy to see that if those individuals that display relatively low fitness do so so that they can help others carrying the same allele to display relatively high fitness, then such an allele under at least some circumstances might outcompete other alleles that fail to display such properties.
Key to inclusive fitness is for alleles that give rise to reduced fitness in some individual, such that others may display enhanced fitness, only provide that fitness boost to others that happen to also carry the same fitness-boosting allele. The simplest means of assuring that others likely carry similar alleles is to display such behaviors predominantly or exclusively towards relatives, i.e., with individuals that by definition carry similar alleles. This logic forms the basis of the idea of kin selection, where cooperative interactions take place predominantly with relatives, thereby assuring to a degree that they occur among individuals possessing the same cooperation-enhancing alleles. In terms of microbial evolution, evolutionary ecology, and population biology, it is important to note that clonally related individuals essentially share all of their alleles.
The idea of a selfish gene is basically that of a nucleotide sequence that enhances its fitness, and particularly its numbers, at the expense of whatever is carrying that sequence. In essence, such genes basically are parasitic, though these are parasites that are somewhat limited in their virulence if their potential to replicate independently of the organism within which they reside is somewhat limited. In other words, the more closely the fitness of an individual gene is tied to the fitness of the organism harboring that gene, then the lower the potential for that gene "get away" with being selfish. Alternatively, any gene that can replicate independently of a given organism, which at an extreme can include genes that simply are found in other organisms, may be able to exploit those non-harboring individuals without cost (e.g., as predators exploit prey organisms). In between these two extremes can be found various selfish genes, which are able to enhance their own interests over those of their hosts to a degree, but ultimately are still dependent upon their hosts retaining a reasonable potential to survive and reproduce.
Be careful, though, when using "selfishness" to describe what essentially is the basis of an "altruistic" behavior (i.e., inclusive fitness). What this is saying is that the genes (alleles) are placing their own success above that of their carriers/hosts (i.e., being selfish) but they are accomplishing this feat, in terms of inclusive fitness, by in fact making their hosts act less selfishly towards others. So long as you and others understand that point, then it's OK to use selfishness and inclusive fitness in the same sentence, but otherwise confusion may occur.