Microbiologists are faced with the daunting task of understanding the diversity of life forms that cannot be seen with the naked eye but can live anywhere on Earth. Obviously a reliable classification system is paramount.
The science of classifying living things is called taxonomy (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern). In a broader sense, taxonomy consists of three separate but interrelated parts: classification, nomenclature, and identification.
A taxonomic scheme is used to arrange organisms into groups called taxa (s., taxon) based on mutual similarity. Nomenclature is the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules.
Identification is the practical side of taxonomy—the process of determining if a particular isolate belongs to a recognized taxon and, if so, which one.
The term systematics is often used for taxonomy, although it sometimes infers a more general scientific study of organisms with the ultimate objective of arranging them in an orderly manner.
Thus systematics encompasses disciplines such as morphology, ecology, epidemiology, biochemistry, genetics, molecular biology, and physiology.
One of the oldest classification systems, called natural classification, arranges organisms into groups whose members share many characteristics.
The Swedish botanist Carl von Linné, or Carolus Linnaeus as he often is called, developed the first natural classification in the middle of the eighteenth century.
It was based largely on anatomical characteristics and was a great improvement over previously employed systems because natural classification provided information about many biological properties.
For example, classification of humans as mammals denotes that they have hair, self-regulating body temperature, and milk-producing mammary glands in the female.
When natural classification is applied to higher organisms, evolutionary relationships become apparent simply because the morphology of a given structure (e.g., wings) in a variety of organisms (ducks, songbirds, hawks) suggests how that structure might have been modified to adapt to specific environments or behaviors. However, the traditional taxonomic assignment of microbes was not rooted in evolutionary relatedness.
For instance, bacterial pathogens and microbes of industrial importance were historically given names that described the diseases they cause or the processes they perform (e.g., Vibrio cholerae, Clostridium tetani, and Lactococcus lactis).
Although these labels are of practical use, they do little to guide the taxonomist concerned with the vast majority of microbes that are neither pathogenic nor of industrial consequence. Our present understanding of the evolutionary relationships among microbes now serves as the theoretical underpinning for taxonomic classification.
In practice, determining the genus and species of a newly isolated microbe is based on polyphasic taxonomy. As the term “polyphasic” suggests, this encompasses many aspects that describe the microorganism. These include phenotypic, phylogenetic (i.e., the evolutionary history), and genotypic features.
To understand how all of these data are incorporated into a coherent profile of taxonomic criteria, we must first consider the individual components.
For a very long time, microbial taxonomists had to rely exclusively on a phenetic system, which classifies organisms according to their phenotypic similarity (See Table). This system succeeded in bringing order to biological diversity and clarified the function of morphological structures.
For example, because motility and flagella are always associated in particular microorganisms, it is reasonable to suppose that flagella are involved in at least some types of motility. Although phenetic studies can reveal possible evolutionary relationships, this is not always the case.
For example, not all flagellated bacteria belong to the same phylum. This is why the best phenetic classification is one constructed by comparing as many attributes as possible.
As the name suggests, genotypic classification seeks to compare the genetic similarity between organisms. Individual genes or whole genomes can be compared.
Since the 1970s it has been widely accepted that bacteria and archaea whose genomes are at least 70% homologous belong to the same species.
However, there is now a consensus building to replace this metric with a genomicsbased assay that measures the average nucleotide identity between organisms. The means by which microbes are genotypically classified is discussed further in section.
With the publication in 1859 of Charles Darwin’s On the Origin of Species, biologists began developing phylogenetic or phyletic classification systems that sought to compare organisms on the basis of evolutionary relationships.
The term phylogeny (Greek phylon, tribe or race, and genesis, generation or origin) refers to the evolutionary development of a species. Scientists realized that when they observed differences and similarities between organisms as a result of evolutionary processes, they also gained insight into the history of life on Earth.
However, for much of the twentieth century, microbiologists could not effectively employ phylogenetic classification systems, primarily because of the lack of a good fossil record.
When Carl Woese and George Fox proposed using small subunit (SSU) rRNA nucleotide sequences to assess evolutionary relationships among microorganisms, the door opened to the resolution of long-standing inquiries regarding the origin and evolution of the majority of life forms on Earth—microbes.
As discussed later, the power of rRNA as a phylogenetic and taxonomic tool rests on the features of the rRNA molecule that make it a good indicator of evolutionary history and on the ever-increasing size of the rRNA sequence database.