Additional topics exists which are relevant to microbiology, and particularly microbial evolution that are worthy of discussion at this juncture. These include issues surrounding the origin of cells, the already mentioned plasmids as well as transposons which together represent semiautonomous genetic entities, and finally a working definition of just what a microorganism consists of such that we can focus particularly on the evolution of microorganisms versus the evolution of entities that in fact are not microorganisms. This section is then followed by one where various microbiology terms are introduced that are commonly seen also in the microbial evolution literature.

Chemical Evolution

Chemical evolution refers especially to evolution that occurred prior to but leading up to the origin of life. That is, before a form existed that could be described as living there must have been replicating and evolving forms for which a consensus among researchers could be reached that in fact they were not alive. The typical way of thinking about chemical evolution is in terms of autonomously replicating RNA (the question of whether or not naked RNA truly was a progenitor replicator being beside the point). Presumably the evolutionary biology of this pre-life evolution resembled at least in part the evolutionary biology that has taken place since the origin of life (sensu stricto). As such, thinking on chemical evolution presumably can inform thinking on microbial evolution, and vice versa. Issues of chemical evolution thus should not be ignored within the context of microbial evolution. To what extent issues of chemical evolution ought to be emphasized is debatable, however. Likely, when considering the evolutionary biology of, for example, viroids or RNA viruses, which arguably are more chemical like and clearly are RNA-containing, then issues of chemical evolution may be more relevant than when considering the evolutionary biology of cellular organisms. For a nice summary of how pre-biotic evolution might have taken place, see Ricardo and Szostak (2009).

Alternatively, the issue of just where bacteria came from, like the issue of where eukaryotes or multicellular organisms came from, evolutionarily, is clearly an issue of microbial evolution. Since chemical evolution, essentially by definition, is concerned with pre-life processes, so too it must be relevant to understanding the transition to life, i.e., to prokaryotic organisms. Thus, chemical evolution has its place within the context of microbial evolution study, but again, to what extent it should be emphasized should be a function of individual preference.

Semi-Autonomous Genetic Entities

Another area of interest within the context of microbial evolution is the evolution of genetically based, semi-autonomous aspects of organisms. These include such things as plasmids and transposons. What these have in common are specific mechanisms of replication that are not identical to the replication of the host genome. As such, these genetic entities have the potential to evolve in ways that are somewhat independent of or even at the expense of their harboring host. Furthermore, some, or perhaps even many, most, or all such entities can be viewed as potentially infectious. In the case of self-transmittable plasmids, this potential for transmission is explicit. Transposons, by contrast, may be transmitted from host to host by piggy backing on the transmission mechanisms of other entities, such as self-transmissible plasmids or viruses. The key distinction between these semi-autonomous genetic entities and viruses thus can be viewed in terms of degree of independence from host fitness: The independence from host fitness cannot be as great for a transposon or a plasmid as it can be for a virus, which can kill its hosts in the course of replication and transmission, and prosper while doing so.

Semantics and distinctions aside, these various genetic entities impact host fitness and host evolution. If those hosts are microbes, then these semi-autonomous genetic entities can clearly play a role in microbial evolution. In addition, these entities can be viewed as simplified selective units, i.e., as compared with cellular organisms or even viruses, so can be related to microbial evolution in the same ways as issues of chemical evolution may be, informing ideas on microbial evolution and vice versa. Lastly, there are important issues regarding microorganisms that may be understood at least in part in terms of microbial evolution, e.g., such as antibiotic resistance among bacteria, which often is associated with semi-autonomous genetic entities such as plasmids. Thus, to integrate microorganisms into evolutionary theory, especially as more than just physiological or genetic "black boxes", it is relevant to consider microbes in terms of not just their basic genomes but also with regard to the genetic accessory elements that also commonly reside within their cells.

Microbes vis-à-vis Microbial Evolution

Microbes have been present for as long as life has existed on Earth, have been highly successful, and otherwise are polyphyletic. As a consequence of these features, there exists a great deal of microbial diversity. Notwithstanding this variety, as a basis of general discussion of microbial evolution I will consider a microorganism to be a unit of selection possessing both phenotype and genotype but which, organismally, is so small that generally it is easier to study group properties than it is to study the properties of individuals (modern techniques of analysis of individual cells being an exception).

Microorganisms possess some degree of autonomy from other organisms such that a transposon or a plasmid, in and of itself, is not a microorganism. Highly integrated obligate endosymbionts such as mitochondria, in turn, straddle the limit of what may be reasonably described as a microorganism. I additionally will take the perspective that at some point in animal, fungal, and algal evolution there was a transition – in terms of both size and the multicellular complexity of individual organisms – such that these entities, other than the unicellular yeasts along with small, single-celled or colonial algae, are not microorganisms, regardless of how small certain examples might be.