GENERAL MICROBIOLOGY - T.P. Pyrog - 2004

7. PROKARYOTE SYSTEMATICS

7.2. TERMINOLOGY USED IN SYSTEMATICS

Nowadays, attempts to address various aspects of the systematics of both individual groups of MICROORGANISMS AND THE entire system as a whole are frequently hindered by contradictions arising from the ambiguity of certain terms. Formalization of terminology is a crucial step in bacterial systematics.

The fundamental concepts and terms used in bacterial systematics were most clearly defined by Academician G.O. Zavarzin of the Russian Academy of Sciences in his monograph *Phenotypic Systematics of Bacteria* (1974).

Systematics is The Theory of organismal diversity that studies the relationships between groups of organisms (classes, taxa).

Classification is the division of a multitude (set) of organisms into groups (classes, taxa).

Taxonomy involves naming groups of organisms (taxa), establishing their boundaries, and defining their hierarchical arrangement.

Nomenclature is a collection of rules for naming taxa, supplemented by a list of these names.

Diagnosis (identification) is the method of finding a given taxon and determining whether an object belongs to that taxon.

Thus, systematics encompasses classification, taxonomy, nomenclature, and identification. Let us examine these concepts in greater detail.

Classification. Various types of classification exist (phylogenetic, phenotypic, genotypic, natural, artificial, etc.), depending on the Goals and Objectives underlying the system. For quite some time, it was believed that modern classifications were phylogenetic, and that a common origin of organisms could be indicated by identical metabolic pathways (based on the premise that each enzyme arose only once during evolution), as well as by an identical Chemical composition of structural Cell components, since each such component reflects a specific biosynthetic pathway. In reality, however, all these classifications were phenotypic, as they were based on similarities in the morphological and physiological properties of organisms.

According to G. Schlegel (1987), There are two types of classifications: natural (phylogenetic) and artificial. Phylogenetic classification reflects evolutionary relationships among organisms. Constructing a phylogenetic classification is the ultimate goal of bacterial systematics. Unlike phylogenetic classification, artificial classification serves solely for the identification of microorganisms and may be limited, for example, based on features that are convenient and useful for Structure/179.html">Practical Applications.

The basic unit of classification is the strain—a pure culture of a bacterium isolated from a natural substrate. Strains are grouped into species, species into genera (singular: genus, plural: genera). Similar genera are grouped into tribes (Latin names ending in *-eae*), and tribes into families (Latin names ending in *-aceae*). A family may comprise genera without any intervening tribes, which is most frequently observed in modern bacterial classification. Families are grouped into orders (Latin names ending in *-ales*), and orders into classes. Classes may be grouped into divisions.

Nomenclature. Unlike the multitude of classifications, bacterial nomenclature undergoes fewer changes because it is governed by international rules. In the second half of the 18th century, Carl Linnaeus proposed nomenclature principles that were adopted by biologists. Later, two nomenclature codes were established: botanical and zoological. For a long time, microbiologists primarily used botanical nomenclature. Finally, in 1930, at the First International Microbiological Congress, a commission on bacterial nomenclature and taxonomy was organized. The Bacteriological Code of Nomenclature was published in 1948. The Sixth Congress in Rome (1953) approved the publication of the International Code of Nomenclature of Bacteria and Viruses. The Ninth International Microbiological Congress (Moscow, 1966) proposed introducing a distinct new system of nomenclature for viruses. A revised Bacteriological Code was adopted by the International Congress of Bacteriology in Jerusalem in 1973 and published in 1975 (in Russian in 1978). However, by that time, microbiology had accumulated many obsolete names for microorganisms. Consequently, the Judicial Commission of the International Committee on Systematic Bacteriology proposed reviewing existing bacterial names to streamline nomenclature. The resulting Materials (Approved Lists of Bacterial Names) were published in 1980 in the *International Journal of Systematic Bacteriology*. Thus, 1980 marked a new milestone in The Development of bacterial systematics, separated by nearly two and a half centuries from May 1, 1753—the starting date for bacterial nomenclature.

For bacteria, just as for plants and animals, binomial nomenclature is used, consisting of generic and specific epithets written in Latin METABOLISM/31.html">Transcription. The genus name is capitalized, while the species name is written in lowercase. As a rule, the species name reflects a characteristic feature or property of that species. For example, *Sarcina flava* or *Bacillus mycoides*.

Identification. Unfortunately, microbiological research utilizes very few standard Methods, and identification is frequently attempted using traits detected by highly Specific methods. However, identification should be based on simple, accessible methods. To this end, dichotomous keys are employed, presenting alternative statements that logically lead to the diagnosis of an unknown Organism.

Identification techniques are clearly and accessibly outlined in Chapters I–V of the ninth edition of *Bergey's Manual of Determinative Bacteriology* (hereinafter referred to as Bergey's Manual). The first edition of this manual was published in 1923 by a group of American bacteriologists led by D.H. Bergey. It should be noted that starting with the ninth edition, this formerly unified work was divided into a four-volume *Bergey's Manual of Systematic Bacteriology* and the concise *Bergey's Manual of Determinative Bacteriology*. It is the latter work that was translated into Russian in 1997 as *Bergey's Manual of Determinative Bacteriology*, used for identifying bacteria based on phenotypic traits and containing condensed information on all bacterial species. Created for practical purposes, this publication does not claim to reflect evolutionary relationships.

Suppose we need to identify an isolated microorganism. The general approach to solving this task consists of several main stages:

1) Bergey's Manual is used for bacterial identification. Therefore, one must first ensure that the isolated isolate is a prokaryote. Chapter III provides a table of traits distinguishing prokaryotes from eukaryotes;

2) in the Manual, all bacteria are divided into four main categories (gram-negative eubacteria with cell walls; gram-positive bacteria with cell walls; eubacteria lacking cell walls; archaebacteria). The traits enabling the determination of these categories are given in Chapter IV;

3) the next step, after determining the main bacterial category, is to identify the section of the Manual in which it is discussed. Chapter V provides a list of groups within each main category and a brief Description of the features of bacteria belonging to each group. Each of the four main bacterial categories is subdivided into groups: the first category consists of 16 bacterial groups (Nos. 1–16), the second of 13 (Nos. 17–29), the third of one group (No. 30), and the fourth of five groups (Nos. 31–35). Thus, the Manual describes a total of 35 bacterial groups;

4) Determination of the bacterial genus. For most groups, tables or keys are provided indicating the traits used to differentiate genera within the group;

5) determination of the bacterial species. Descriptions of most genera contain tables that facilitate the differentiation of species within a given genus.

Taxon. A taxon is the fundamental category in bacterial systematics. The following ranks of taxa are distinguished: division, Class, order, family, genus, species. There are many Definitions of the term "taxon":

any taxonomic group obtained As a result of applying a specific classification method:

a group of organisms characterized by a given degree of homogeneity; a taxonomic group of any rank that is sufficiently distinct to be assigned a separate category.

It should be noted that THE CONCEPT OF a "taxon" always refers to specific organisms. Moreover, a taxon must be formally described in accordance with the rules of the International Code of Nomenclature of Bacteria. According to this code, a taxon consists of one or more organisms. A nomenclatural type must be designated for all taxonomic categories. It does not necessarily have to be the most typical element of the taxon (Rule 15 of the Code). For a species, this is the type strain; for a genus, the type species, and so on. Thus, it is alternatively proposed to consider as the type species: a species that is the sole representative of the genus; a species that was the only representative of the genus in its first publication; a species with which the name of the genus is consistently associated and which, as a rule, is the representative of the genus that is recognized first (most easily recognized).

Most frequently, a systematist deals with such a taxonomic category as a species. As known from biology, The Essence of this concept is difficult to define, so let us examine it in more detail.