## 6.1 Taxonomy of Prokaryotes The study and classification of prokaryotic organisms, revealing their evolutionary history and relationships. Unlike eukaryotic classification, which often relies on morphology, prokaryotic taxonomy heavily utilizes molecular biology. ### Phylogenetics **Phylogenetics** is the study of evolutionary relatedness among various groups of organisms. It traces the origin and evolution (phylogeny) of a set of organisms. In modern taxonomy, the sequence of **16S rRNA** is considered the most reliable method for determining the phylogenetic relationship between two different prokaryotic species because it is highly conserved. ## Historical Classification: The Five-Kingdom System The five-kingdom system was proposed by American biologist **Robert H. Whittaker** in **1969**. This system was based on the fundamental distinction between prokaryotes and eukaryotes. All prokaryotic organisms were grouped into a single kingdom called **Monera**. This system was later revised by Lynn Margulis and Karlene V. Schwartz in 1988 but maintained the Monera kingdom for prokaryotes. ## Modern Classification: The Three-Domain System Advancements in molecular systematics revealed that prokaryotic life consists of two distinct domains that evolved independently from a common ancestor. In **1977**, **Carl Woese** identified that archaea have a separate evolutionary lineage from bacteria, a discovery that fundamentally changed prokaryotic classification. This led to the widely accepted **three-domain system**, which divides all life into: 1. **Bacteria** (formerly Eubacteria) 2. **Archaea** (formerly Archaebacteria) 3. **Eukarya** ### Bergey's Manual of Systematic Bacteriology The standard reference for bacterial classification is **Bergey's Manual**. It classifies bacteria based on shared characteristics such as cell wall composition, morphology, and gram-staining reactions. For example, bacteria with a thin, Gram-negative type cell wall are placed in a specific category (Gracilicutes). ## Evolutionary History of Prokaryotes The ancestors of modern bacteria were single-celled microorganisms that first appeared on Earth approximately **4 billion years ago**. For about **3 billion years**, all life was microscopic, with bacteria and archaea being the dominant life forms. The most recent common ancestor of bacteria and archaea is believed to have lived **2.5 to 3.2 billion years ago** and was likely a hyperthermophile (an organism that thrives in extremely hot environments). ## Internal Structures and Taxonomy While taxonomy focuses on classification, understanding the internal ultrastructure is vital for identifying prokaryotic groups. ### Mesosomes The **mesosome** is an invagination of the plasma membrane in the form of vesicles, tubules, or lamellae. It plays a role in DNA replication, cell division, and export of exocellular enzymes. ### Polysomes In prokaryotes, several ribosomes can be seen attached to a single mRNA strand during protein synthesis. This complex is known as a **polysome**.