Microorganisms come in a great variety, which is a reflection of their phylogenetic diversity. That is, there are lots of ways to be small, both ancestral and derived. The obvious categories of microorganisms, especially from a medical perspective, are the bacteria and viruses. Medically relevant microorganisms, however, also include various single-celled eukaryotes, including yeasts, protozoa, and eukaryotic algae. Important environmentally, if not necessarily also medically, are the Archaea and the cyanobacteria, both of which are prokaryotes (cellular organisms lacking cell nuclei), though the Archaea are otherwise unrelated to the bacteria (i.e., domain Bacteria) while the cyanobacteria, by contrast, are members of domain Bacteria. Together these cellular organisms are formally classified as being members of domains Eukarya, Archaea, or Bacteria.
Other microbe types, not necessarily technically organisms, include viroids and prions, which consist only of naked RNA and only naked protein, respectively. The latter, i.e., prions, are not really microbes, though they nonetheless are infectious, just as certain infectious cancers, such as that seen with the Tasmanian devil, are not microbiological, but nevertheless microbe-like in that they are infectious diseases. Finally, as noted, are the parasitic worms, which are animals. Conspicuously missing from the above list are the plants, though even they are closely related to microbes (i.e., the eukaryotic, single-celled green algae) plus exhibit single-celled stages that temporarily exist in isolation from their multi-celled parents, i.e., the flagellated sperm produced by the non-seed-bearing plants. In short, there exists a continuum going from the microorganisms through the macroorganisms, with the dividing line between the two more arbitrary than you might imagine.
One the three cellular domains, the Bacteria (or, simply, bacteria), traditionally have been the primary emphasis of microbiological studies and their medical concerns. This is because, of the cellular organisms, bacteria are both the most ubiquitous, which is to say most common in human-containing environments, and most likely to give rise to infectious disease, especially in animals such as humans. Bacteria are prokaryotes, meaning that their cells lack nuclei (see below for discussion of the legitimacy of the term prokaryote). Thus, bacteria have a simpler cellular structure than seen with eukaryotes. That simplicity is also observed as an absence or, at least, relative absence of a cytoskeleton as well as a relative dearth of membrane-enclosed intracellular compartments.
Bacteria generally have cell walls, though this is not always the case (e.g., the bacterial genus Mycoplasma). The cell walls typically are differentiated into Gram-positive versus Gram-negative types, with Gram-positive bacteria having thicker cell walls and only one enclosing membrane, the plasma or cytoplasmic membrane, which is found internal to the cell wall. The Gram-negative bacteria, by contrast, have thinner cell walls and two enclosing membranes. These include the inner membrane, which is equivalent to the plasma membrane and, as with Gram-positive bacteria, is found inside of the bacterium's cell wall, and the outer membrane, which is more permeable and which lies outside of the bacterium's cell wall. An additional category of cell "walls", which is based on staining characteristics during light microscopy, is the acid-fast cell envelope, a feature of certain soil as well medically important bacteria including, especially, members of genus Mycobacterium (e.g., M. tuberculosis).
Bacteria typically are not multicellular, though certain cyanobacteria – formerly called blue-green algae – approximate simple multicellularity. Bacteria usually have relatively simple shapes, including spherical (cocci), elongated (bacilli), curved (vibrios, helical, or spirochetes), plus many bacteria can be found as cellular arrangements, e.g., staphylococci or streptobacilli (or streptococci). Certain aquatic bacteria, ones perhaps adapted to obligately planktonic life styles, however, can display complex surface-area enhancing morphologies. See Young (2006; 2007) for fascinating consideration of the adaptive values (essentially the evolutionary ecology) of bacterial shape.
Many bacterial cells have also appendages, though these usually are not enclosed by the plasma membrane (contrast many eukaryotic cellular appendages) and also these appendages can be difficult to see using light microscopy without special staining techniques, e.g., pili and flagella, as well as capsules (which arguably are not strictly appendages but rather cell coatings). These extra-plasma membrane structures can be involved in attachment, motility, and protection, respectively. Bacteria can also differ in size, though generally members of domain Bacteria have smaller cells than do members of domain Eukarya.
Microbes are often characterized in terms of their metabolic attributes. Most notable among those attributes are such things as from what they obtain their energy (e.g., photons or glucose) from what they obtain reduced carbon (e.g., carbon dioxide or glucose), their oxygen requirements (anaerobes, aerobes, etc.), the physical conditions under which they can reproduce (including ranges as well as optima such as in terms of temperature, pH, and osmolarity), etc. Thus, for example, bacteria (as well as other organism types) can be described as chemoheterotrophs or photoautotrophs, which are organisms that obtain their energy and carbon from the molecules associated with other organisms versus organisms that obtain their energy from light (photo) and their carbon from CO2 (autotrophy). Among bacteria there are also chemoautotrophs (which obtain energy from mostly inorganic molecules and carbon from CO2) and photoheterotrophs (which obtain energy from light but not reducing power).
Oxygen requirements can vary from obligate dependence on oxygen (aerobes or obligate aerobes) to oxygen serving instead as a fatal toxin (strict or obligate anaerobes) to indifference to oxygen's presence (aerotolerant anaerobes). Oddly, some aerobes can replicate under anaerobic conditions, but either way are obligately dependent on electron transport systems to generate ATP. Alternatively, facultative anaerobes can employ electron transport systems under aerobic conditions but also may employ fermentative pathways (rather than electron transport systems) under anaerobic conditions. The latter includes the bacterium Escherichia coli, which also has the characteristics of being a Gram-negative, chemoheterotrophic bacterium.
Members of domain Archaea have been noted especially for their abilities to occupy niches displaying extreme physical conditions or, at least, extreme from our own vantage. These include high temperatures (exceeding in some cases the sea level boiling temperature of water), low pH, and high salt concentrations (up to and including saturated NaCl). These organisms are also often found in anaerobic environments, including in particular methanogens.
Methanogens, by way of example, convert hydrogen gas – or in some cases simple organic compounds such as acetate – along with carbon dioxide into methane gas, which constitute important fractions of swamp gas as well as bovine flatulence. Hydrogen here serves as the electron donor while carbon dioxide serves as the electron acceptor, with both necessary for methanogen energy generation. These chemicals furthermore are found in the methanogen-containing environments because they are waste products that have been produced by other, non-methanogenic organisms or, in the case of CO2 , can represent products of physical processes.
Alternatively, there are less-well studied archaea that inhabit less extreme environments, such as sea water. Together, archaean metabolisms include photo- as well as chemotrophic and hetero- as well as autotrophic, plus aerobic as well as anaerobic varieties (as discussed above, these respectively are obtaining energy from photons/light, obtaining energy from chemicals, fixing CO2 to produce organic carbon, consuming the products of other organisms in order to obtain organic carbon, employing oxygen as a final electron acceptor during the generation of ATP along with the generation of membrane potentials, and use of something other than oxygen as a final electron acceptor). Notably, the gene-expression apparatus of archaea tends to be more similar to that of members of domain Eukarya than to those of domain Bacteria. This observation is perhaps indicative of an evolutionary origin of eukaryotes from a member of domain Archaea, perhaps as merged with a Bacteria endosymbiont.
Eukaryotes, the members of domain Eukarya, are organisms whose cells contain nuclei as well as other membrane-enclosed compartments such as the endoplasmic reticulum, the Golgi apparatus, lysosomes, etc. Eukaryotes also contain more complex membrane-enclosed organelles such as mitochondria and chloroplasts. Because of the size of their bodies and indeed also of their individual cells, eukaryotes are the most conspicuous organisms on Earth. Whether protozoa, eukaryotic algae, yeasts, or, arguably, even parasitic worms (helminths), the eukaryotes are also important microorganisms. In fact, the vast majority of eukaryotes are microorganisms, and greater genetic diversity exists among the eukaryotic microorganisms than among the so-called crown eukaryotes, which are the animals, plants, and fungi. This greater genetic diversity is seen in with the more microscopic eukaryotes essentially despite the obvious morphological diversity seen with these multicellular, crown eukaryotes. Thus, to truly understand eukaryote evolution, in toto, one must understand microbial evolution.
This latter claim is true for yet additional reasons. The first is that the origin of eukaryotes is something that took place within the context of microbial evolution and which therefore involved microorganisms. The second is that an extremely important aspect of eukaryote evolution, and one that continues to this day, is the formation of symbioses with microorganisms, including endosymbioses particularly with bacteria. Lastly, there exists ongoing evolution within eukaryote lineages that involves microorganisms, whether viruses transmitting DNA between lineages or bacteria (and smaller eukaryotes) conveying their own genomes, via a series of accidents, into the genomes of eukaryote hosts or consumers. Indeed, perhaps the most fascinating aspect of eukaryote evolution is their acquisition of endosymbiotic bacteria that not only perform important or essential metabolic tasks for their eukaryotic hosts but also gradually (over millennia) lose their genomes as their genes are transferred to the nuclear genome of the eukaryote host. In some cases, the bacteria remain, functional and "replicating", with no internal genome at all!
The term "Prokaryote" is used to distinguish organisms that have the property of lacking nuclei, that is, a cell nucleus, from organism that instead possess nuclei, that is, the eukaryotes. As such, at least in my opinion, the term prokaryotes is both legitimate and an historically relevant one. The problem with the idea of prokaryotes, as a taxon, is that it is phylogenetically invalid. That is, as a taxon, "prokaryote" is not monophyletic, meaning that at least some of its members are more closely related (seemingly) to organisms found outside of the taxon than they are to organisms found within it. Specifically, members of domain Bacteria and domain Archaea do not naturally coalesce into a taxon that excludes members of domain Eukarya. This is a legitimate objection to the use of the term prokaryote taxonomically. Therefore, my use of this term is less formal or strict, meaning solely those cellular organisms that are not members of domain Eukarya, which arguably is a more microbiological perspective, that is, versus a taxonomic, phylogenetic, or evolutionary biological perspective. Note, for accuracy's sake, that one could describe prokaryotes, taxonomically, as paraphyletic if we assume that eukaryotic organisms evolved from prokaryotic ancestors, just as birds evolved from reptilian ancestors (thus making reptiles, as a taxon that does not include the birds, also paraphyletic).
Viruses, contrasting members of domains Archaea, Bacteria, or Eukarya, are not cellular organisms. Arguably, they in fact are not even organisms. Instead, viruses consist of nucleic acid that has been encapsidated at least by protein. The so-encapsidated viral genomes are then responsible for acquiring new cellular hosts, which they infect cell by cell. Viruses are unable to replicate without infecting these cells intracellularly and as such can be described as obligate intracellular parasites. Other obligate intracellular parasites include certain bacteria as well as viroids. Viruses are usually encapsidated by a protein shell known as a capsid. Capsids come in a variety of morphologies including filamentous, polyhedral (often icosahedral), and a mixture of the two that can described as complex but which also is known as tailed. Capsids for certain virus types can be also be found in association with lipids, which especially for animal viruses is a lipid bilayer known as an envelope.
The function of the virion – the mature, genome-containing capsid which, in many cases, is also enveloped – is protection of the genome during the virus extracellular state combined with host attachment and subsequent genome uptake into the host cell's cytoplasm. The second aspect of the virus life cycle begins at this point and involves expression of virus-genome-encoded genes, takeover of host-cell metabolism, subsequent virus-genome replication, packaging of the resulting progeny genomes to create virion particles, and then release of those particles into the extracellular environment. In the course of all of this action, what viruses do not encode nor possess, except by stealing from cells, are ribosomes, most basic metabolic pathways, or plasma membranes. The limited metabolic activity of viruses on the one hand limits their versatility, e.g., such as in terms of behavioral or physiological adaptation, but on the other hand allows viruses, under the right circumstances, to display much higher fecundities than cellular organisms.
Also distinguishing viruses from cellular organisms are virus genomes. Quantitatively, viral genomes mostly are smaller than those of cellular organisms, possessing fewer genes, though larger viruses have genomes that are larger than those of the smallest cellular genomes. In addition, the larger viruses have genomes that are well over 100-fold the size of the genomes of the smallest viruses (the overall range of virus genome sizes actually is from a bit more than 1 kb to approximately 1,000 kb, whereas the smallest cellular genomes are in the range of 500 kb and range up to well over 10-fold larger for bacteria alone). Qualitatively, virus genomes are notable for their employment of unusual forms of nucleic acid. These include chemical modifications of that nucleic acid, but also the use of RNA (rather than DNA) as genomes plus the use of ssDNA as well as dsRNA. With few exceptions, for a given virus a genome will either be RNA or DNA and single-stranded or double-stranded, all as packaged within the viral particle, but across the totality of viruses all such genome types exist. In addition, depending on the virus, genomes can be monopartite (a single chromosome) or multipartite (multiple chromosomes, typically described as segments). Consistent with this virus "experimentation" with genome characteristics, it has been argued that viruses "invented" DNA itself, which only subsequently was co-opted by cellular organisms.
Phenotypically, perhaps the key virus characteristic is its host range, which is a description of the kinds of cellular organisms a virus is capable of employing as a host. Typically virus host ranges are relatively narrow, and because of this most viruses may be distinguished in terms of the broader category of hosts that they are capable of infecting. Thus there exist animal viruses as well as plant viruses. There are viruses also which infect protozoa. The viruses that are limited to infecting members of domain Bacteria are described as bacteriophages, or phages. The viruses of domain Archaea, by contrast, are mostly known instead as archaeal viruses. Within these larger groupings, virus host ranges also tend to be relatively limited, typically to only one or a few host species, or for phages in many cases only a limited number of bacterial strains within a larger species. One can also speak of the types of cells within a multicellular organism that a virus is capable of infecting, a property known as a virus' tropism.
Viral infection involves virus takeover of host functions. The degree of take over varies from virus to virus, with some viruses more dependent on normal host functioning whereas other viruses are less dependent. Those that are less dependent on host functions typically have to either bypass or replace those functions. In general, viruses that possess larger genomes, and therefore which have greater numbers of viral genes, are less dependent on host functions than are those viruses with smaller genomes and therefore fewer genes. In any case there nonetheless will exist a diversity of host machinery – such as that involved in ATP generation (e.g., electron transport systems) and protein synthesis (such as ribosomes) – the continuing operation of, viruses are highly dependent upon during infection.
Viroids are pathogens of plants. They are like viruses except that they are not encapsidated. Instead, their extracellular state consists of naked RNA. Because they have nucleic-acid based heredity, however, from the perspective of microbial evolution viroids can be viewed as extreme microbes in the sense that they explore the absolutely minimum unit that could be described as being an autonomous life form. Compare viroids, for example, to other genetic entities, such as plasmids, which are either less autonomous or not autonomous at all. (Interestingly, even these other intracellular genetic entities also can be infectious as well as semi-autonomous from their host cells, so perhaps the question of "what is life?" can be reduced even further, with a perhaps not unreasonable endpoint being Dawkin's idea of the "selfish gene".) Another example of an unencapsidated infectious unit are certain "viruses" of fungi (mycoviruses) which are both much larger than viroids and consist of dsDNA rather than ssRNA.
Contrasting viroids, or for that matter, contrasting viruses as well as all cellular life forms, are entities known as prions, which are infectious but which lack genetic material. Instead prions are a form of infectious protein, able to commandeer pre-formed cellular proteins, converting those proteins into additional prions. Because of this, prions display a kind of heredity, and perhaps even evolution. They also certainly are infectious, and because of this they unquestionably are a topic worthy of discussion within the context of microbiology. Since prions lack nucleic acid, and are best understood in terms of how they affect eukaryotes, and often higher eukaryotes at that, from the standpoint of microbial evolution prions may perhaps be best viewed as diseases that happen to have an infectious nature rather than as entities that are highly representative of microorganisms or of microbial evolution.