While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows. — Carl R. Woese (1994)
An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. — Richard E. Lenski et al. (1998)
Evolution is not a blind watchmaker or any other kind of engineer, but rather a short-order cook, and – looking at the phenomenally complicated structures – one who is less like Isaac Newton than Rube Goldberg or W. Heath Robinson… Just look at the [biological] details, and you'll immediately abandon all thoughts that biological systems were designed with any intelligence whatsoever. — Chris Miller (2005)
Microbial evolution, to a first approximation, is a somewhat straightforward subject, consisting of some combination of microbiology and evolutionary biology. Complications immediately arise, however, since neither microbiology nor evolutionary biology are clear-cut subjects. Furthermore, much insight can be lost if one limits one's divagations to the strictly microbiological. The latter, in part, is because the biology of microorganisms may be only artificially separated from that of more macroorganisms. My objective, however, is to concentrate on bacteria (more generally, "prokaryotes"), viruses, and relatively "simple" eukaryotes. In considering what microorganisms interact with or, indeed, what they have evolved into, contemplation of the higher eukaryotes – plants, animals, fungi, and other multicellular creatures – however is difficult to avoid.
Evolutionary biology can be similarly difficult to pin down. In fact, one can very easily distinguish evolutionary processes into so-called microevolution versus macroevolution, that is, evolution that takes place below versus above the level of species. In between is the process of speciation itself, which naturally begs the important question of just what species are. Then there is the "problem" that evolution does not occur within a vacuum but instead has an ecological context. Evolution also is limited by historical contingencies: where you can go often depends upon where you currently are, which in turn is a function of where you previously have been. Evolution in addition inevitably involves tradeoffs that complicate the optimization of adaptations. The study of adaptations has its own subspecialty called, at least as more loosely defined, evolutionary ecology.
The application of all of the above to microorganisms is very complex, in part, because the concept of "microorganism" has little phylogenetic meaning. Microbiology instead is the study of a collection of entities that have been thrown together into an amalgamation of convenience, and this convenience in part is due to an historical dearth of interest by biologists who have preferred to view their research subjects with their own (unaided) eyes. This amalgamation can be seen, in part, with Whitaker's five-kingdom system of organismal classification, where eukaryotic microorganisms are lumped into only a portion of a single kingdom, called Protista, versus a kingdom each for plants, animals, and fungi. Meanwhile, the majority of the world's cellular organisms, what today we describe as domains Bacteria and Archaea – essentially everything but the eukaryotes, making up domain Eukarya – were afforded only a single kingdom, Monera. My desire is not to fault these microorganism-deemphasizing views, since they made reasonably good sense historically, but instead to bring home the point that microbiology is more complicated than necessarily is commonly appreciated, as so too is the evolution of microorganisms.
A concept has been invented that takes into account much of the above-noted complications: microbial population biology. The beauty of microbial population biology, as a concept, is that it is about microorganisms (but not necessarily entirely so), it is about evolution (but hardly limited to evolution sensu stricto), and, perhaps most importantly, it is about microbial ecology, but without forcing upon the participant intense consideration of microbe-based ecosystem ecology. The latter is the movement of nutrients and energy among organisms, in this case of nutrient cycles. Such movement occurs, for example, within the carbon cycle, which is often global in its nature and which to an important degree involves microorganisms, as essentially all nutrient cycles do. Microbial population biology instead focuses, not surprisingly, on the population biology of microorganisms. There thus is concern about the molecular/physiological aspects of microorganisms, especially as these contribute to their organismal properties, but this is not done in isolation of the organism's ecology or evolution. There also is consideration of microorganism-to-microorganism interactions, which can be viewed not just on a population level (i.e., intraspecific interactions), but also at the level of communities (i.e., interspecific interactions) or even in terms of ecosystems (in the sense of movement of nutrients and energy from one organism to another). One, however, never strays too far from the microorganism itself as an evolving individual and, above all, an evolutionarily self-interested entity in its own right. Consideration of these individuals – or more strictly populations of such individuals – is the essence of microbial population biology. It in turn is an important component of our emphasis here.
In Chapter 2, "Population Biology", I provide quick overviews of what the disciplines of evolutionary biology, ecology, and evolutionary ecology are all about. I save for Chapter 3, "Microbiology", the introduction to microbiology. The latter represents an abridged overview as may be found in an introductory microbiology text, though without emphasis on specific microbe species, molecular aspects, or disease. Together Chapters 1, 2, and 3 should be viewed as background reading for individuals approaching these subjects more from the microbiological or more from the evolutionary biological (or ecological) sides of that all-too-common divide among biologists between molecular/reductionism, on the one hand, and organismal/ultimate causation interests on the other. Greater depth of consideration of evolutionary biology, both from a more general, i.e., not specifically microbiological, as well as more microbiology-specific perspectives are presented in Chapters 4 and 5. Chapter 4, "Non-Darwinian Forces", in particular covers mutation, genetic drift, and migration – often described, as indicated by the title, as non-Darwinian evolutionary mechanisms – while Chapter 5, "Natural Selection", covers instead Darwinian mechanisms. To those who are especially knowledgeable of both microbiology and evolutionary biology, and who are looking to skip chapters, I nonetheless would encourage at least a skimming of Chapters 4 and 5.
In Chapter 6, "Evolution of Resistance", especially these latter issues are again presented, particularly from a microbial perspective. They are then applied to the issue of evolution of microbial resistance such as to antiobiotics. As such, this chapter represents a bridge chapter between what in many cases at least arguably could be background material and that material – found in subsequent chapters – which constitutes the core of the course.
Chapter 7, "Passage through Time", provides an overview of how microbial population biology may be studied experimentally, especially in terms of ongoing microorganism growth along with associated ecology and evolution. The presented approaches are rather than such things as in situ diversity determinations, e.g., metagenomics, or more thorough molecular analyses including isolate sequencing that typify what today may be described as traditional (or typical) microbiological approaches. The former (metagenomics) I would describe as more a purview of microbial ecology or of environmental microbiology than of microbial population biology. It is not that diversity determinations are not important for understanding microorganisms from a population perspective. It instead is that the emphasis of metagenomics – by necessity due to incomplete sampling of available sequence – tends to be on community characteristics rather than those of individual populations, whereas better approximation of complete sequencing of a single environmental sample could allow substantial comparison within individual populations. On a per-locus basis, however, such approximations of complete sequencing may be achieved via PCR-based analyses of environmental samples. Prominence in metagenomic analyses tends to be placed on determining molecular aspects, i.e., genes, rather than on more whole organismal facets, including spatial arrangements of organisms on microscales, though the latter can be derived from metagenomic data sets by using FISH, fluorescence in situ hybridization, to visualize the location of individual, metagenomically derived sequence. Notwithstanding these caveats, it is impressive how much biology can be inferred from sequence "snapshots" alone.
The rest of the book is devoted mostly to consideration of the consequences of organism-to-organism interaction. This begins with a key theme, that of "Gene Exchange", as covered in Chapter 8. That is, sex. I next reflect on how genomes are shaped by evolution, in Chapter 9, "Genomes". The emphasis there is not only that genomes change going from generation to generation, but also that a surprisingly large amount of the evolution impacting genome structure in microorganisms is tied to gene exchange or its absence. These two chapters (8 and 9) may be viewed as transitions between the first and second halves of the book. For example, genomes can be viewed as conglomerations of cooperating genetic entity (mostly genes), and the principles of the study of cooperation and their application to microorganisms, beyond just gene-gene interactions, is found in Chapter 10, "Cooperation".
The final three chapters consider the evolution of specific kinds of organism-to-organism interactions. First are cooperative interactions seen with symbioses, which occur between microbes and larger (host) organisms as well as among microorganisms themselves. This is covered in Chapter 11, "Symbioses", where coverage of endosymbionts, e.g., such mitochondria and plastids, is also found. Chapter 12, "Virulence", takes the opposite tack, considering how, and why, natural selection can favor symbiotic interactions that result in damage especially to the host organism. Finally, in Chapter 13, "Greater Size and Complexity", the previous analyses of microbial gene exchange, cooperation, symbiosis, and virulence are combined to provide insight into the evolution of the non-microbial, i.e., organisms, particularly eukaryotes, that are larger and more complex as well as multicellular. It turns out that we have not moved all that far beyond our "inner microorganism", though we have learned a few tricks necessary to keep the latter's worst tendencies at bay.