MICROBIOLOGY - M.H. Serhiichuk - 2008

CHAPTER 7. SYSTEMATICS OF MICROORGANISMS

Principles of Bacterial Classification

The first attempt at a scientific Classification of microorganisms was made by the Danish zoologist O. Müller, who defined all the main morphological forms of Bacteria. In his proposed classification, all species known at the time were divided into two genera: Monas and Vibrio.

C. Ehrenberg (1795-1876) in his book "Infusoria as Perfect Organisms" (1838) divided the Class of infusoria into 22 families, three of which encompassed bacteria. We encounter names such as Spirillum, Spirochaeta, and Bacterium in his work, which are still used in modern systematics. He was the first to apply the binomial nomenclature principle to microorganism species names. Among the still-known species described by Ehrenberg are the hay bacillus (Bacillus subtilis) and Spirillum volutans. He also first described the "miracle bacterium" (Bacterium prodigiosum, modern name Serratia marcescens),

which caused panic by appearing as bloody spots on starchy foods ("bloody bread").

The early classification schemes for bacteria were based on cataloging, where microorganisms were grouped into taxa solely on The basis of morphological traits. Over time, however, it became clear that studying morphological characteristics alone was insufficient for a satisfactory distribution of bacteria into taxonomic groups. The necessity of using PHYSIOLOGICAL AND BIOCHEMICAL traits alongside morphological features for bacterial classification was established by S. Winogradsky and M. Beijerinck.

Studying the morphological and cultural properties of a microorganism is the first step in its classification. This involves examining Cell shape and size, colony Morphology (Fig. 7.5), and growth characteristics in liquid culture media.

In recent years, two main trends have emerged in the classification of prokaryotes. The first is based on developing a phylogenetic system of bacteria—that is, creating a unified system that objectively reflects evolutionary relationships among different prokaryotic groups, taking into account their historical development. The second trend focuses on practical goals, aiming to serve for the rapid identification of prokaryotes, meaning the assignment of an Organism to a specific taxon. This second approach is clearly evident in Bergey's Manuals of Determinative Bacteriology.

To develop a phylogenetic system of prokaryotes similar to those of plants and animals (the traditional evolutionary tree), initial attempts relied on phenotypic traits. All utilized traits were conditionally categorized by their relative importance. Subsequently, based on these weights, objects were sorted into taxonomic groups. Consequently, it is easy to see that The Structure of such a hierarchical system is determined by the order in which traits are arranged, while this very order is chosen arbitrarily (subjectively).

All of this prompted systematists to seek alternative approaches for determining the degree of bacterial relatedness. To eliminate elements of subjectivity, numerical Taxonomy was proposed, the foundational principles of which were developed as early as 1757 by the French botanist M. Adanson (1727-1806). Numerical taxonomy rests on the principles that every character is of equal weight when evaluating an individual (equivalence of characters); descriptions of the studied culture must incorporate as many features as possible; the degree of similarity is a function of the number of shared characters; and individual assessment and classification are based on character correlation.

Fig. 7.5. Some forms of bacterial colonies:

a - blistered; b - folded; c - wrinkled; d - foamy; e - concentric; f - fluffy; g, h - filamentous; i - rhizoid; j, k - "fried egg"; l - flat with a wavy marginal ridge; m - circular, smooth, glistening; n - smooth, irregular; o - circular with a marginal ridge

Bacterial classification built on Adanson's principles is a rather labor-intensive Procedure and thus only truly developed and found Practical Application with the advent of computers. Its advantages lie in the formal ability to partially eliminate subjective bias, as all traits are deemed equally valuable. The drawback of this approach is

incomplete information content: assessing bacterial similarity relies on about 100 traits, which constitutes roughly 10% of those defining the bacterial phenotype. This principle forms the basis of the internationally recognized Bergey's Manual of Determinative Bacteriology.

Bacterial manuals are designed with practical application in mind. All manuals by D. Bergey (1860-1937) were prepared following this principle. The first edition was published in 1923, and the ninth edition—"Bergey's Manual of Systematic Bacteriology"—appeared in 1984-1986. Recent editions are prepared by the American Society for Microbiology with the involvement of leading systematists worldwide. Notably, starting with the 9th edition, this previously unified work was split into the 4-volume taxonomic reference "Bergey's Manual of Systematic Bacteriology" and the 2-volume identification manual "Bergey's Manual of Determinative Bacteriology".

According to the ninth edition, all bacteria are united under the kingdom Procaryotae and divided into four main categories. This division is based on the presence and STRUCTURE OF THE Cell wall, with each category uniting specific groups of bacteria.

Category I. Graciliscuta (Lat. gracilis - slender; cutes - Skin) - Gram-negative eubacteria possessing cell walls. This category unites groups 1 through 16. Cells may be oval, straight or Curved Rods, spirals, or filaments. Some may be covered by a sheath or capsule. Reproduction occurs primarily via binary fission, occasionally by budding. In some representatives (e.g., Pleurocapsales), cell multiplication occurs through multiple internal divisions, producing small spherical cells called baeocytes (nanocytes). Myxobacteria can form fruiting bodies and myxospores. This division includes both motile and non-motile forms, with motility occurring via swimming or gliding.

Category II. Firmicutes (Lat. firmus - strong) - Gram-positive eubacteria possessing cell walls. This category unites groups 17 through 29. Cells are spherical, rod-shaped, or filamentous; rods and filaments occasionally branch. They typically reproduce by binary fission. Some representatives form resting spores (endospores) or spores on hyphae. This division includes asporogenous and spore-forming bacteria, as well as actinomycetes and related organisms.

Category III. Tenericutes (Lat. tener - delicate, soft) - eubacteria lacking a cell wall. Commonly known as Mycoplasmas, they are assigned to the class Mollicutes (group 30). All of them are incapable of synthesizing peptidoglycan precursors. Their cells are bounded solely by a Plasma Membrane, highly pleomorphic, and vary widely in size. They reproduce by budding, fragmentation, and/or binary fission. Most are non-motile, though some exhibit gliding motility. They do not stain by Gram's method and require complex media for growth, forming characteristic "fried egg" colonies on solid nutrient media.

Category IV. Mendosicutes (Lat. mendosus - false) - archaea. These are prokaryotes whose cell wall structure lacks true peptidoglycan. These bacteria are characterized by metabolic diversity and The ability to thrive in extreme environments. They are predominantly found in anaerobic, hypersaline, or hydro- and geothermally heated habitats. Archaea can be either mesophiles or thermophiles, with some species capable of growing at temperatures above 100⁰ C. They stain either Gram-positive or Gram-negative. In Gram-positive archaea, The Cell wall consists of pseudomurein, methanochondroitin, and Heteropolysaccharides. Cell shapes can be spherical, spiral, plate-like, or rod-like. Cell thickness ranges from 0.1 to ~15 µm, and length can reach up to 200 µm.

Advances in biochemistry and molecular biology have made it possible to develop alternative approaches for determining the degree of bacterial relatedness. One such approach is based on the comparative study and alignment of the Introduction/19.html">Primary Structure of macromolecules involved in the cell's most vital Functions. These macromolecules include DNA, RNA, and enzyme Proteins. It is known that Genetic information is "encoded" in DNA molecules as various combinations of three out of four nitrogenous bases. According to the laws of genetic coding, distinct information cannot be coded identically; therefore, organisms with different nucleotide compositions in their DNA will be different. If the Nucleotide Composition of two compared organisms is identical, they may still be either similar or dissimilar, because genetic coding relies not only on a specific base content within a coding unit (triplet) but also on their mutual arrangement.

For taxonomic purposes, researchers compare the molar percentage of guanine-plus-cytosine (G+C) content relative to the total base content of DNA from various sources. It has been found that the GC content in plants and animals varies within a narrow range of 35-40 mol%, whereas in bacteria it ranges from 25 to 75%. Uniquely, the average GC base content among strains of the same species is very close or nearly identical. This regularity

has been proven for many bacterial groups, including Representatives of the genus Pseudomonas (Table 7.2). Within this genus, the range of variation is also quite limited, not exceeding 10-15%. This regularity allows the GC content value to be used in streamlining the classification of certain bacterial taxonomic groups.

However, such G+C content does not always indicate a phylogenetic relationship between organisms. For instance, Pseudomonas aeruginosa and Mycobacterium phlei both contain 60 % GC. Therefore, other Methods are used to determine the similarity (relatedness) of organisms more accurately. Greater expectations in prokaryotic systematics are placed on the DNA-DNA Hybridization method, which allows a quantitative Assessment of the degree of Homology between the genomes of compared organisms. The method is based on the ability of denatured (single-stranded) DNA under certain conditions to reassociate—that is, to join with a complementary strand and form a double-stranded molecule. The amount of double-stranded DNA formed As a result of the interaction between single-stranded DNAs isolated from different organisms serves as an indicator of their relatedness.

Table 7.2. G+C content in various strains of certain species of the genus Pseudomonas

In addition to DNA analysis for establishing the degree of relatedness among prokaryotic organisms, methodical approaches have been developed that allow the comparison of products of individual genes that perform identical functions within the cell. These can be proteins (such as ferredoxins, Cytochromes, etc.) or rRNA. Choosing rRNA to solve the problems of evolutionary systematics in prokaryotes is advantageous for several reasons: these molecules are found in all Cellular forms of life; their functions remain constant; and their primary structure is characterized overall by high conservation. It is known that the Ribosomes of both PROKARYOTES AND EUKARYOTES contain Three types of rRNA, which differ in molecular weight and sedimentation coefficient. Larger molecules have a higher information capacity, but they are more difficult to analyze. Therefore, the 16 S rRNA molecule (in prokaryotes) and the 18 S rRNA molecule (in eukaryotes) have proven to be the most suitable. Based on the obtained results, similarity coefficients for the compared organisms were calculated, revealing not two groups of organisms differing in prokaryotic and eukaryotic Cellular Organization, but three (Table 7.3). The first group comprises all eukaryotes: higher plants, animals, Yeasts, Algae, Fungi, etc. Eukaryotic Organelles (Mitochondria, METABOLISM/14.html">Chloroplasts) are excluded from this group. The second group, designated as true bacteria (eubacteria), encompasses the vast majority of prokaryotes. Based on 16 S rRNA homology levels, the Mitochondria and chloroplasts of eukaryotes also fall into this category. The third group includes prokaryotes (primarily inhabitants of extreme environments) composed of macromolecules, most of which are unique and synthesized by neither eukaryotes nor bacteria. This group was named archaebacteria. Based on this characteristic, it has been proposed to divide All living organisms into three superkingdoms or domains: Eukaryota, Eubacteria, Archaebacteria.

Table 7.3. Main characteristics of archaebacteria, eubacteria, and eukaryotes

On January 1, 1980, the International Code of Nomenclature of Bacteria (ICNB) was established.

According to the ICNB, new taxon names must be effectively published in generally accessible literature, but a new taxon is considered validly published only if its description appears as a separate article in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Improperly published new taxa must be presented in quotation marks.