Science of Classification
Taxonomy is the scientific study of naming and categorizing living organisms based on shared characteristics. Plants, animals, and microbes are sorted into categories based on molecular and physiological similarities and evolutionary relatedness. Classification is an important subset of taxonomy that involves the arrangement of these groups into hierarchies. These hierarchies provide important information about an organism and allow scientists to easily study the relationships between groups. Nomenclature is the branch of taxonomy that uses rules to assign names to groups of organisms.
In the 1700s, Carl Linnaeus, a Swedish botanist, invented a simple system for naming organisms that revolutionized the field of taxonomy. This system, called binomial nomenclature, is a two-word naming convention for each type of organism, which includes a genus and species name. The genus and species can be abbreviated as the first letter of the genus followed by the species. For example, humans are classified as Homo sapiens, or H. sapiens. Genus and species names are very specific, but organisms are also organized into more general groups, including family, order, class, phylum, kingdom, and domain. The classifications assigned to organisms within this standard hierarchy are regularly updated and changed as researchers learn new information about organisms and the evolutionary relationships among them. The advent of technologies in the late 20th century allowing molecular characterization of organisms has resulted in substantial reorganization of traditional taxonomies that are based on visible characteristics.Taxonomic Hierarchies
Taxonomy of Microorganisms
All life can be classified into three domains: Archaea, Bacteria, and Eukarya. Both Archaea and Bacteria are made up of prokaryotes, which are single-celled microbes that lack a nucleus. The domain Archaea is made up of ancient microorganisms (microbes) that live in extreme conditions. Domain Bacteria contains the bacteria, most of which have rigid cell walls. An exception to this is the genus Mycoplasma, which does not have a cell wall. The domain Eukarya contains single-celled and multicellular organisms that have a nucleus and other membrane-bound organelles. The kingdoms Fungi (e.g. yeast and molds), Plantae (e.g. green plants), Animalia (humans and other animals), and the many groups that were historically classified as Protista (e.g. algae and amoeba) are all part of the domain Eukarya.
Prokaryotic species are defined in a slightly different way from eukaryotic species of higher organisms. Because microbes do not always reproduce sexually, they do not exist as isolated groups of interbreeding populations. Instead they must be grouped by similarities and differences in their observable characteristics and genetic content. Viruses are not included in any of the three domains of life, as they are not considered to be living.
Three Domains of Life
| Archaea | Bacteria | Eukarya | |
|---|---|---|---|
| Cell Type | Prokaryotic | Prokaryotic | Eukaryotic |
| Multicellular | No | No | Some |
| Autotrophic | Some | Some | Some |
| Cell Wall | Pseudopeptidoglycan | Peptidoglycan | Some (examples: cellulose, chitin) |
The three domains of life are differentiated by their cell type, whether they are multicellular, and whether they have a cell wall and the material used to construct it.
Classification of microbes is constantly improving with the development of new methods and technology. Ways that scientists identify microbes include:
- looking at morphology (structural characteristics),
- differential staining (use of chemical stains to highlight cell characteristics),
- biochemical testing (differentiating cells based on activities, such as fat metabolism, protein metabolism, etc.)
- deoxyribonucleic acid (DNA) sequencing (determining the order of nucleotides in a DNA molecule).
Morphology describes a set of visible characteristics, such as size and shape. Some microbes can also be identified by the presence of structures on their surface (and in some cases, internal structures) that can be viewed under a microscope after differential staining.
Biochemical tests provide more detailed information about a microbe, such as the types of nutrients it can consume or what enzymes it produces. Bacteria can be grown on selective media, which contain nutrients and additives, that inhibit the growth of some microbes while allowing others to grow. Additionally bacteria can be grown on differential media, which uses different visual cues to differentiate between bacteria species. A medium can be selective and differential, for example eosin methylene blue (EMB) agar. Methylene blue is toxic to gram-positive cells and prevents their growth, thus selecting for gram-negative cells. EMB is also a differential medium; if bacteria ferment lactose, the EMB appears purple, while those that do not ferment lactose appear clear. There are many different enzyme assays (tests for measuring enzyme activity) that can give important information about what group a particular microbe belongs to. The catalase test is an example of an enzyme assay that allows scientists to determine whether a bacterium contains the enzyme catalase, which is used to break down hydrogen peroxide.
DNA can be isolated from microbes and sequenced to look for genes and other genetic features of known microbes. In particular the GC content, or percentage of the nucleic acid bases guanine (GTP) and cytosine (CTP) in the genome, varies between different groups of microbes and can be useful for classification.