Fundamentals of Microbiology

Lesson 7. CLASSIFICATION, NOMENCLATURE AND IDENTIFICATION

Module 3. Microbial taxonomy

Lesson 7

CLASSIFICATION, NOMENCLATURE AND IDENTIFICATION

7.1 Introduction

Taxonomy (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern) is defined as the science of biological classification. In a broader sense it consists of three separate but interrelated parts: classification, nomenclature, and identification.

7.1.1 Identification

Identification is "the practical side of taxonomy, the process of determining that a particular (organism) belongs to a recognized taxon."

7.1.2 Classification

Classification is "the arrangement of organisms into groups or taxa."

7.1.3 Nomenclature

Nomenclature is "the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules.

7.2 History of Taxonomy

Earlier Concept: The ancient Greek philosopher Aristotle apparently began the discussion on taxonomy. Aristotle divided organisms into plants and animals. He subdivided them by their habitat - land, sea, or air dwellers.

John Ray (1627–1705): British naturalist John Ray is credited with revising the concept of naming and describing organisms. He was the first to use Latin for naming. The names given by him were very long descriptions telling everything about the plant. He was an English naturalist, sometimes referred to as the father of English natural history. He published important works on plants, animals, and natural theology. His classification of plants in his Historia Plantarum, was an important step towards modern taxonomy. He coined the term species.

Carolus Linnaeus (1707–1778), Linnaeus, 18th century taxonomist, classified organisms by their structure. He is credited with developing the modern system of naming known as binomial nomenclature and is called the ‘Father of Taxonomy’.

Two-word name (Genus and species)

– Genus species
– Latin or Greek
– Italicized in print
– Capitalize genus, but NOT species
– Underline when writing

Carolus Linnaeus distinguished two kingdoms of living things: Animalia for animals and Vegetabilia for plants (Linnaeus also included minerals, placing them in a third Kingdom, Mineralia). He divided each kingdom into classes, later grouped into phyla for animals and divisions for plants.

Edouard Chatton (1883-1947), a French biologist, contributed to our knowledge of single-celled protoctists, especially ciliates and dinoflagellates, free-living and/or symbiotic, in relation to the marine invertebrate animals in which they reside. More than the description of many new families, genera and species, and of their life cycles, he anticipated several major concepts of cell biology, including the fundamental difference between prokaryote and eukaryote protists, long time before the advent of electron microscopy. It gradually became apparent how important the prokaryote/eukaryote distinction is, and Stanier and van Niel popularized Chatton's proposal in the 1960s to divide them.

Ernst Heinrich Philipp August Haeckel (1834–1919), was an eminent German biologist, naturalist, philosopher, physician, professor and artist who discovered, described and named thousands of new species, mapped a genealogical tree relating all life forms, coined many terms in biology, including phylum, phylogeny, ecology and the kingdom Protista. In 1866, Ernst Haeckel divided animals, plants, and microorganisms into 3 kingdoms namely Animalia, Plantae and Protista.

Robert Harding Whittaker (1920–1980), recognized an additional kingdom for the Fungi. The resulting five-kingdom system, proposed in 1969, has become a popular standard and with some refinement is still used in many works and forms the basis for newer multi-kingdom systems. It is based mainly on differences in nutrition; his Plantae were mostly multicellular autotrophs, his Animalia multicellular heterotrophs, and his Fungi multicellular saprotrophs. The remaining two kingdoms, Protista and Monera, included unicellular and simple cellular colonies.

In biological taxonomy, kingdom and/or regnum is a taxonomic rank in either (historically) the highest rank, or (in the new three-domain system) the rank below domain. Each kingdom is divided into smaller groups called phyla (or in some contexts these are called ‘divisions’). Currently, many textbooks from the United States use a system of six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea, Bacteria) while British and Australian textbooks may describe five kingdoms (Animalia, Plantae, Fungi, Protista, and Prokaryota or Monera). The classifications of taxonomy are life, domain, kingdom, phylum, class, order, family, genus, and species.

7.3 Classification Systems

Hierarchical classification: In classification taxonomist follow a hierarchy of designations; means in ascending sequence. The full description of a given organism's place among all the world's organisms does not end with its binomial designation. There exists a hierarchy of designations only the last of which describe genera and species denomination. A category in any rank unites groups in the level below it based on shared properties. The major designations, listed in terms of increasing specificity, include

• Domain (empire/super-kingdom)
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

 

Example

Genus: Escherichia

Species: coli

Family: Enterobacteriaceae

Class: Scotobacteria

Division: Gracilicutes

Kingdom: Procaryotae

7.3.1 Five kingdoms of life

Living organisms as suggested by are subdivided into 5 major kingdoms, including the Monera, the Protista (Protoctista), the Fungi, the Plantae, and the Animalia (Fig. 7.1). Each kingdom is further subdivided into separate phyla or divisions. Generally ‘animals’ are subdivided into phyla, while ‘plants’ are subdivided into divisions. These subdivisions are analogous to subdirectories or folders on your hard drive. The five kingdom system of classification for living organisms, including the prokaryotic Monera and the eukaryotic Protista, Fungi, Plantae and Animalia is complicated by the discovery of archaebacteria. The prokaryotic Monera include three major divisions: The regular bacteria or eubacteria; the cyanobacteria (also called blue-green algae); and the archaebacteria. Lipids of archaebacterial cell membranes differ considerably from those of both prokaryotic and eukaryotic cells, as do the composition of their cell walls and the sequence of their ribosomal RNA subunits. In addition, recent studies have shown that archaebacterial RNA polymerases resemble the eukaryotic enzymes, not the eubacterial RNA polymerase.

7.3.2 Six kingdoms

Around 1980, there was an emphasis on phylogeny and redefining the kingdoms to be monophyletic groups, groups made up of relatively closely related organisms. The Animalia, Plantae, and Fungi were generally reduced to core groups of closely related forms, and the others placed into the Protista. Based on RNA studies, Carl Woese divided the prokaryotes (Kingdom Monera) into 2 kingdoms -Eubacteria and Archaebacteria. Carl Woese attempted to establish a 3 Primary Kingdom system in which Plants, Animals, Protista, and Fungi were lumped into one primary kingdom of all eukaryotes. The Eubacteria and Archaebacteria made up the other two kingdoms. The initial use of ‘six kingdom system’ represents a blending of the classic five kingdom system and Woese's three domain system (Fig. 7.2). Such six kingdom system has become standard in many works. A variety of new eukaryotic kingdoms were also proposed, but most were quickly invalidated, ranked down to phyla or classes, or abandoned. The only one which is still in common use is the kingdom Chromista proposed by Cavalier-Smith, including organisms such as kelp, diatoms, and water moulds. Thus the eukaryotes are divided into three primarily heterotrophic groups, the Animalia, Fungi, and Protozoa, and two primarily photosynthetic groups, the Plantae (including red and green algae) and Chromista. However, it has not become widely used because of uncertainty over the monophyly of the latter two kingdoms.

7.3.3 Three domain system

In 1970, Carl Woese, by analyzing RNA, developed the 3 domain classification system (Fig.7.3)

• Archaebacteria
• Bacteria
• Eucarya

Woese stresses genetic similarity over outward appearances and behaviour, relying on comparisons of ribosomal RNA genes at the molecular level to sort out classification categories. A plant does not look like an animal, but at the cellular level, both groups are eukaryotes, having similar subcellular organization, including cell nuclei, which the Eubacteria and Archaebacteria do not have. More importantly, plants, animals, fungi, and protists are more similar to each other in their genetic makeup at the molecular level, based on RNA studies, than they are to either the Eubacteria or Archaebacteria. Woese also found that all of the eukaryotes, lumped together as one group, are more closely related, genetically, to the Archaebacteria than they are to the Eubacteria. This means that the Eubacteria and Archaebacteria are separate groups even when compared to the eukaryotes. Therefore, Woese established the three domain system, clarifying that all the Eukaryotes are more closely genetically related compared to their genetic relationship to either the bacteria or the archaebacteria, without having to replace the ‘six kingdom system’ with a three kingdom system. The three domain system is a ‘six kingdom system’ that unites the eukaryotic kingdoms into the Eukarya Domain based on their relative genetic similarity when compared to the Bacteria Domain and the Archaea Domain. Woese also recognized that the Protista kingdom is not a monophyletic group and might be further divided at the level of kingdom. Others have divided the Protista kingdom into the Protozoa and the Chromista, for instance.