General Microbiology - Schlegel, H. G. 1987

Prokaryotes: A Systematic Review
Introduction

Based on the previously mentioned characteristics—such as the absence of a nuclear membrane, limited compartmentalization, and the presence of a peptidoglycan Cell wall—all organisms formerly classified under the Schizophyta (specifically the Schizomycetes, or Bacteria in the broadest sense, and the Schizophyceae, or blue-green Algae/cyanobacteria) can be grouped together into a single prokaryotic domain (Procaryotae). Their description and nomenclature are governed by the International Code of Nomenclature of Bacteria, which is developed and overseen by the International Committee on Systematic Bacteriology. Unlike the Botanical Code, the Bacteriological Code stipulates that the description of a new strain must be accompanied by the deposition of a viable culture in an officially recognized culture collection, serving either as a reference strain or a type strain.

Description of bacteria. When describing bacteria, the primary step is to outline their morphological characteristics: whether they are cocci, rods, or spirilla; whether they possess a capsule; whether individual Cells form aggregates (such as filaments, tetrads, or clusters); whether flagella are present and how they are arranged; whether the bacteria form endospores; and how they react to Gram staining. This morphological description is then complemented by a list of key PHYSIOLOGICAL AND BIOCHEMICAL traits, specifying: 1) oxygen requirements (i.e., whether the cells grow under aerobic, anaerobic, or facultative conditions); 2) METABOLISM/26.html">Energy Metabolism (Respiration, Fermentation, or Photosynthesis); 3) Temperature and pH growth ranges, including optimum values; 4) utilized nutrients; 5) habitats; 6) symbiotic or parasitic associations; 7) intracellular inclusions, pigmentation, and capsule composition; 8) cell wall components (peptidoglycan backbone, lipopolysaccharides, teichoic^[ acid); 9) serological differentiation (surface Antigens, homologous Proteins); 10) DNA base composition (mol% G+C); 11) DNA-DNA Hybridization and transformability during interspecies DNA transfer; 12) nucleotide sequences of 16S or 5S rRNA; and 13) antibiotic sensitivity.

Nomenclature. Similar to plants and animals, bacteria are designated using a binomial nomenclature consisting of a generic and a specific name. The original rule—that generic names should reflect morphological traits while specific names reflect physiological ones—was eventually abandoned following major scientific breakthroughs. Aided by the staggering metabolic diversity of bacteria, Beijerinck and Winogradsky began assigning generic names based on ecological, physiological, and biochemical features. For instance, physiological traits were used to name genera such as Acetobacter, Nitrosomonas, and Azotobacter; pigmentation for Chromobacterium and Rhodomicrobium; pathogenicity for Pneumococcus and Phytomonas; and utilized substrates for Haemophilus and Amylobacter. In accordance with nomenclature rules, names proposed in valid original descriptions must be upheld. The assignment and usage of names are strictly regulated.

Classification. The classification of prokaryotic microorganisms primarily prioritizes practical utility, serving as a tool to identify and distinguish already described forms. Classification involves organizing units into higher-level groups following a hierarchical framework. The fundamental unit is the pure culture of an isolated bacterium, known as a "strain." Strains are grouped into species, species into genera (singular: genus), and genera into families (with Latin family names ending in -aceae). An adequate description of strains forms The basis of classification, enabling meaningful comparison and differentiation. Taxonomy is the scientific discipline dedicated to establishing the hierarchical relationships among these organismal groups.

Two MAIN TYPES OF classification must be distinguished: phylogenetic (or "natural") classifications on the one hand, and artificial ones on the other. Developing a natural classification is the ultimate goal of bacterial taxonomy: to group related forms linked by a common evolutionary origin and thereby construct a Phylogenetic Tree of bacteria. Undoubtedly, this will eventually be achieved using chemical markers, such as the Amino acid sequences of functionally homologous Enzymes or The nucleotide sequences of conserved Nucleic Acids like Ribosomal RNAs.

Artificial classification pursues more modest objectives than phylogenetic classification. It is content with grouping organisms based on overall similarity and is primarily utilized for identification and diagnostic purposes. Artificial systems are essentially designed to function as diagnostic keys. The most comprehensive compendium of bacterial descriptions is Bergey’s Manual of Determinative Bacteriology, the eighth edition of which was published in 1974. It contains bacterial names, descriptions of their morphological and physiological properties, literature citations, and keys for identifying newly isolated forms. A new edition is currently in preparation¹.

Numerical taxonomy. The next step toward a more objective system is "numerical taxonomy." This approach is based on Adansonian principles, which posit that all observable and quantifiable characters hold equal weight in characterizing an Organism. To obtain a quantitative assessment, as many characters as possible are evaluated and selected in an alternative format—meaning their variants can be scored with a "plus" or "minus." These character combinations are processed using computers, comparing every trait of one strain against every trait of all other strains. The overall similarity between two examined strains is considered greater as The ratio of matching characters to the total number of evaluated characters increases.

Pairwise comparisons rely on the similarity coefficient (value $S$), which is calculated as follows:

Class="center">

where $a$ and $d$ represent the sums of characters for which strains A and B agree ($a$ denotes both positive, $d$ denotes both negative); $b$ is the sum of characters for which strain A is positive and strain B is negative; and $c$ is the sum of characters for which strain A is negative and strain B is positive. The resulting values range from 0 to 1. $S = 1$ indicates 100% similarity (identity), whereas $S < 0.02$ denotes absolute dissimilarity. These values are compiled into a similarity matrix and can also be visualized as a dendrogram (resembling a phylogenetic tree). However, numerical taxonomy has no direct bearing on phylogeny.

¹ Volume 1 of the new edition appeared in 1984, followed by Volume 2 in 1986 under the title Bergey’s Manual of Systematic Bacteriology. — Editor's note.

Bacterial phylogeny. Ribosomes are the sites of Protein Synthesis AND are therefore present in all cells. Functionally, they are highly conserved, particularly regarding ribosomal RNAs (rRNAs), since their base sequences are largely insulated from the degeneracy of The Genetic Code and suppressor Mutations. Consequently, rRNA fulfills all the criteria required of a universal phylogenetic marker. Nucleotide sequencing of 16S rRNA across a wide range of bacteria has revealed both unexpected divergences and striking similarities. Cataloging these nucleotide sequences has yielded similarity coefficients ($S_{ab}$ values), culminating in a dendrogram that can legitimately be regarded as a phylogenetic tree. This approach has uncovered previously unknown evolutionary relationships. For instance, close affinities have emerged between certain phototrophic and non-phototrophic Gram-negative bacteria—such as the relatedness of Rhodopseudomonas sphaeroides¹ and R. capsulata to Rhizobium and Paracoccus denitrificans; Chromatium to Pseudomonas, Azotobacter, and Escherichia coli; Rhodopseudomonas gelatinosa² to Alcaligenes; and finally, the affinity of Rhodomicrobium vannielii, Rhodopseudomonas viridis, and R. acidophila with Mitochondria. This demonstrates that aerobic Gram-negative bacteria trace their origins back to multiple lineages of phototrophic bacteria. Thus, the long-held assumption that aerobic bacteria evolved from a single phototrophic Lineage is refuted by rRNA sequence analysis.

Furthermore, this analysis led to the surprising Conclusion that one specific bacterial group differs profoundly from all others: it appears that the prokaryotes diverged very early into two distinct branches—one comprising the archaebacteria, and the other encompassing all remaining groups collectively designated as eubacteria:

Thus, it is hypothesized that ancestral cells (progenotes) gave rise to archaebacteria on one hand and eubacteria on the other. Additionally, there is evidence suggesting close evolutionary links between archaebacteria and eukaryotes.

Overview of prokaryotic diversity. This overview aims to provide students encountering these topics for the first time with a comprehensive picture of prokaryotic diversity. We will closely follow the 8th edition of Bergey’s Manual of Determinative Bacteriology, which organizes bacteria into 19 groups. However, this manual does not cover cyanobacteria, nor were the findings that led to the recognition of archaebacteria known at the time of its publication. In light of numerous recent discoveries, further taxonomic revisions and additions can be safely anticipated. What will undoubtedly remain stable, however, are microscopically visible characteristics. Similarly, oxygen requirements ($O_{2}$ dependency) and Gram-staining reactions are relatively straightforward to determine.

As a preamble to our Structure/133.html">Discussion of prokaryotes, we provide a table grouping eubacteria by Morphology (cocci, rods, and spirilla/Curved Rods), oxygen requirements (aerobic vs. anaerobic), and Gram-staining properties. To maintain continuity with Bergey’s Manual, the original group numbering has been retained. Bacteria that cannot be easily assigned to one of these three primary morphological categories are listed in the table under the heading "Major Special Groups."

¹ = Rhodobacter sphaeroides. — Editor's note.

² = Rhodocyclus gelatinosus. — Editor's note.

Subsequent sections (3.2–3.20) will examine various bacterial groups in the exact order presented in the table. While certain groups will be described only briefly, cross-References will be provided to the physiological and biochemical sections of this book where those same organisms are discussed in greater detail. A slightly more thorough description is reserved here only for groups that receive little or no coverage in the physiological chapters.

This overview of the prokaryotic system already points the way toward bacterial identification. As most biologists know from experience, identification keys can only identify organisms that are already familiar to some extent. Bacterial identification invariably requires a broad knowledge base; therefore, if a rod-shaped bacterium isolated from yogurt somehow keys out as Methanobacterium, there is every reason to be skeptical!