MICROBIOLOGY Study Guide - 2012

CHAPTER 4. PROKARYOTE SYSTEMATICS

A vast number of microorganisms are systematically arranged according to their similarities, differences, and mutual relationships. This is the focus of a science known as systematics (from the Greek systematicos — ordered).

Systematics is the science of organismal diversity that studies the relationships between groups of organisms (taxa). The main branches of systematics are Classification and Nomenclature.

Classification is the orderly arrangement of a multitude of organisms into systematic groups. The tasks of classification include describing microbial species, establishing Phylogenetic relationships among individual groups, and elucidating speciation processes.

Nomenclature defines the principles for naming established taxa.

A taxon is a group of organisms possessing a specified degree of uniformity. The basic taxonomic unit in microbial systematics is the species.

A species is a group of closely related organisms sharing a common origin, genotype, morphological, physiological, and other characteristics, and capable of inducing identical processes under specific conditions. If deviations from the typical Properties of the main species are observed during The Study of Bacteria, such cultures are regarded as subspecies. The name of a subspecies consists of the full species name, an abbreviation denoting the intermediate taxon (subspecies — subsp.), and the epithet specific to that subspecies. For example, Lactobacillus delbrueckii ssp. bulgaricus — the Bulgarian subspecies of the dairy bacterium.

Taxonomic arrangement of biological groups employs a hierarchical Structure:

Class="center">Domain (Domain) → Phylum (Phylum) → Class (Class) → Order (Order) → Family (Family) → Genus (Genus) → Species (Species) → Subspecies (Subspecies)

Currently, the classification of All living organisms recognizes three domains (superkingdoms): Bacteria, Archaea, and Eukarya.

In addition to subspecies, microbial variants are also distinguished, which do not fit into the hierarchical ranking of classification. They are based on minor hereditary differences among individuals, such as antigenic properties (serovar/serotype), physiological traits (biovar), susceptibility to Bacteriophages (phagovar), and others.

Along with these taxonomic categories, microbiology frequently employs the terms "culture", "strain", and "clone".

A culture refers to microorganisms isolated from a human, animal, plant, or environmental source and grown on a nutrient medium under laboratory or industrial conditions.

A strain is a culture of the same species isolated from different sources, or from the same source at different times, and characterized by minor variations in properties. Differences between strains do not exceed species limits.

A clone is a culture (or population) of microorganisms originating as the progeny of a single Cell.

Following the Discovery of the microbial world, the classification of microorganisms was initially based on morphological features: cell shape and size, endospore formation, Gram-staining characteristics, motility, etc.

Currently, the identification of microorganisms is based on the following criteria:

✵ morphological characteristics;

✵ Cell Structure (prokaryotes or eukaryotes);

✵ cultural characteristics (growth patterns on Solid and liquid media);

✵ physiological properties;

✵ biochemical properties;

✵ molecular-biological properties (percentage of GC and AT pairs in the DNA molecule, nucleic acid Hybridization, 16S ribosomal RNA nucleotide sequence analysis);

✵ chemotaxonomy (Chemical composition of various compounds and structures);

✵ serodiagnosis (determination of antigen—antibody reactions, which is particularly characteristic of pathogenic microorganisms);

✵ phage typing (use of specific bacteriophages).

As established in the 1960s, all organismal properties are determined by unique DNA molecules; consequently, bacteria can be classified by comparing their genomes. Initially, taxonomic comparisons relied on the molar percentage of guanine-plus-cytosine (GC) content relative to the total number of nitrogenous bases in an Organism's DNA. The DNA Specificity coefficient, i.e., The ratio of GC to AT, serves as an important criterion for differentiating genera. For instance, the specificity coefficient is 2.57 for the genus Sarcin, 1.09 for Escherichia, and 0.51 for Streptococcus. However, the GC content provides only a rough comparison of genomes. A more refined method for assessing genetic relatedness among organisms is the comparison of nucleotide sequences in DNA isolated from different specimens. While this method is well-suited for classifying organisms at the species level, it has limited utility for classifying higher-level taxa.

Genetic Methods for microbial identification are based on comparing nucleotide sequences of various genes and analyzing DNA Restriction fragment length polymorphism resulting from the Amplification (generation of multiple copies) of individual bacterial genes. The most suitable targets for identification are the genes encoding 16S and 23S Ribosomal RNAs, as they are ubiquitous in Bacterial Cells and genus-specific. Specialized instrumentation has been developed for the genetic identification of microorganisms. In particular, the MicroSeq system (by Applied Biosystems) identifies bacterial species through automated sequencing (determining the primary DNA nucleotide sequence) of the universal 16S rRNA Gene, which is the primary marker for bacterial taxonomic classification. Following RNA gene sequencing, the system automatically compares the obtained data against MicroSeq microbial libraries. Software algorithms determine the percentage similarity between the unknown bacterial species and the closest reference strains in the library. This equipment enables microbiological quality control of food products alongside the identification of their constituent microorganisms.

Currently, Bergey's Manual of Determinative Bacteriology is widely used for the identification of prokaryotic microorganisms.

The 9th edition of Bergey's Manual of Determinative Bacteriology (1997) proposes a scheme for dividing the kingdom Procariotae into higher taxa based on Cell wall architecture. According to this classification, all microorganisms are divided into four main categories.

1. Gracilicutes (from Lat. gracilis — slender, cutes — Skin) — comprises Gram-negative eubacteria possessing cell walls. These walls consist of an outer membrane, a thin inner peptidoglycan layer, and various additional components located externally or between these two layers.

2. Firmicutes (from Lat. firmis — robust) — encompasses Gram-positive bacteria featuring cell walls composed of peptidoglycan, teichoic, and teichuronic acids.

3. Tenericutes (from Lat. tenerus — soft, delicate) — eubacteria lacking cell walls, known as Mycoplasmas, which include the class Mollicutes. They stain Gram-negative.

4. Mendosicutes (from Lat. mendosus — faulty) — includes archaebacteria that share certain molecular features with eukaryotes but differ in having an imperfect cell wall containing pseudomurein instead of murein. Due to the absence of murein in their cell walls, archaebacteria are resistant to lactam Antibiotics. Archaebacteria are subdivided into the following groups: methanogens; sulfate reducers; extreme halophiles lacking cell walls; and extreme thermophiles that metabolize sulfur.