Systematic Biology and Classification

Classification of Living Organisms

• Systematic biology involves providing scientific names, descriptions, preserving collections, classification, identification, and studying evolutionary histories and environmental adaptations.

History of Classification

• Aristotle (384-322 BC) divided the living world into two kingdoms: plants and animals.
• The two-kingdom system persisted for over 2000 years.
• By the 19th century, the microscope revealed tiny single-celled organisms, leading to the creation of a third kingdom, Protista.
• Protista included bacteria, algae, and fungi.

Development of Classification Systems

• In 1938, Protista was divided into two kingdoms: Monera (unicellular prokaryotic microorganisms, including bacteria) and Protista (eukaryotic microorganisms, including algae and fungi).
• In the 1940s, biologists divided living organisms (except viruses) into two distinct groups: Prokaryotes (bacteria) and Eukaryotes (all other organisms).
• Prokaryotes have cells that lack a nucleus and other cell organelles.
• Eukaryotes consist of cells that contain nuclei and other organelles.

The Three-Domain System

• The three-domain system is currently used, replacing the old five-kingdom system.
• Domain Bacteria and Domain Archaea comprise the prokaryotes.
• Domain Eukarya includes all eukaryotic organisms.

Classification Levels

• There are eight levels of classification: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.

Binomial Nomenclature

• Carolus Linnaeus devised the Binomial Nomenclature system for naming organisms.
• The system uses two names: genus and species (e.g., Gray wolf - Canis lupus).
• Canis lupus is native to North America and Eurasia.

Taxonomy

• Includes classification and nomenclature
• Based on phenotypic characteristics (morphological, physiological, and chemical)
• The basic unit is the species
• Similar species are classified in a single genus and related genera are placed in a single family

Classification

• Bacteria are grouped in the domain Bacteria to separate them from Archaea and Eucarya
• Classification is based on relationships best elucidated by knowledge of evolutionary facts
• However, little is known about phylogenetic relationships, so classification is often based on similarities among phenotypic characteristics
• Chemical characteristics are growing in importance, e.g., murein composition or presence of certain fatty acids in the cell wall
• DNA and RNA structure are highly important in classification
• DNA composition can be estimated by determining the proportions of bases (mol/l of guanine + cytosine, GC)
• DNA-DNA hybrids provide information on the similarity of different bacteria and their degree of relationship
• Sequence analysis of 16S/23S rRNA or rDNA is highly useful in determining phylogenetic relationships

Morphological Characteristics

• Microscopic morphology: cell shape, size, arrangement, staining, capsule characteristics, spore morphology, and flagellar arrangement
• Colonial morphology: colonial appearance, color, shape, texture, margin, and elevation

Biochemical Tests

• Examples: fermentation/oxidation of carbohydrates, enzyme activities, metabolism of organic acids, lipids, proteins, and amino acids
• pH or redox range of growth and tolerance of chemical agents
• These tests collectively define nutritional and physiological interactions of the organism with its environment

Identifying Bacteria

• Dichotomous keys used for morphological identification of organisms
• Differential staining: Gram staining, acid-fast staining
• Biochemical tests: determine presence of bacterial enzymes

Nomenclature

• Rules are set out in the International Code for the Nomenclature of Bacteria
• A species is designated with two Latinized names, the first of which characterizes the genus and the second the species
• Family names always end in -aceae
• Taxonomic names approved by the "International Committee of Systematic Bacteriology" are considered official

Hierarchy

• Species
• Genus
• Family
• Order
• Class
• Division
• Phylum
• Kingdom (1969)
• Domain (1980s)

Phylogeny or Systematics

• Shows evolutionary relationships and history among organisms
• Some obtained from fossil record
• Most bacteria use rRNA sequencing or other sequence information
• A goal is to identify all organisms by 2025

The 5 Kingdoms

• Based on nutrient procurement
• Plantae: multicellular photoautotrophs
• Animalia: ingestive
• Fungi: absorptive
• Protozoa: mostly single-celled
• Prokaryotes: bacteria

Phage Typing

• Determining a strain's susceptibility to certain phage or bacterial viruses

Genetics

• DNA base composition: guanine + cytosine moles% (GC)
• DNA fingerprinting: electrophoresis of restriction enzyme digests
• rRNA sequencing
• Polymerase Chain Reaction (PCR)
• DNA Hybridization