4.14 The Three Domains of Life

• Taxonomy is the practice of biological classification
• The phylogenetic classification system enables us to arrange species into groups based on their evolutionary origins and evolutionary relationships
• By grouping organisms into taxa, it can make them easier to understand and remember
• There are several different ranks or levels within the hierarchical classification system used in biology
  • There is no overlap between groups
  • Each group is called a taxon (plural taxa)
  • Multiple smaller taxa can be put in the same larger taxa
• Species is the lowest taxonomic rank in the system
  • Similar species can be grouped in a genus
  • Similar genera can be grouped in a family
  • Similar families can be grouped into an order
  • Similar orders can be grouped into a class
  • Similar classes can be grouped into a phylum
  • Similar phyla can be grouped into a kingdom
  • Similar kingdoms can be grouped into a domain
• Domains are the highest taxonomic rank in the system
  • They include the Archaea (prokaryotes), Eubacteria (prokaryotes) and Eukarya (eukaryotes)
• There are a few different rhymes that exist to help you remember the different ranks in the taxonomic classification system. You can always make up your own but the one below is super helpful!
  • The first letters of all the different ranks below the domains can be remembered as:
    • Kings Play Chess On Fancy Gold Squares
    • Kingdom Phylum Class Order Family Genus Species

The different levels within the hierarchical classification system - the higher ranks contain more organisms with less similarity between them, while the lower ranks contain fewer organisms with more similarity between them

• Many different species with similar genotypes and phenotypes can be grouped together in the same genus
• They are, however, still separate species since they cannot produce fertile offspring 
  • This is known as the species concept
• Early classification systems only relied on the outward appearance (phenotype) of organisms to classify them
  • Looks can be deceiving however as many non-related organisms share similar phenotypes - e.g. whales and sharks
  • Advances in technology, such as DNA sequencing, have made it possible to compare the genotypes of organisms and provide clarity on the evolutionary relationships between them

Binomial system

• Binomials are the scientific names given to individual species
• It consists of the organism’s genus and species name in modern Latin
  • The genus name is written first and is capitalised, while the species name comes second and is not capitalised
  • Both parts of a binomial are italicised
• For example, the binomial for humans is Homo sapiens and the binomial for dogs is Canis familiaris
• Binomials are extremely useful for scientists as they allow for species to be universally identified - the binomial for a species is the same across the entire globe

Five kingdoms

• Organisms can be placed into one of five kingdoms
• This is based on the general features that groups of organisms within these kingdoms share

Kingdom Prokaryotae (Monera)

• These are organisms that have prokaryotic cells which contain no nucleus
• They vary in size over a wide range, but are typically less than 5 μm
• Example: Staphylococcus pneumoniae is a bacteria species that causes pneumonia

Kingdom Protoctista

• All Protoctista are eukaryotic, and this broad group of cellular life encompasses all eukaryotic cells that do not belong to the other three eukaryotic kingdoms
• Members of this kingdom show great diversity in all aspects of life including structure, life cycle, feeding, trophic levels and modes of locomotion
• They usually live in aquatic environments
• Protoctists can exist as single-celled organisms or as a group of similar cells
• A group of Protoctista known as protozoa possess cells similar to animal cells
  • Their cells have no cell wall
• Another group of Protoctista known as algae possess cells similar to plant cells
  • Their cells have cellulose cell walls and chloroplasts
• Stentor roseli is a protoctist that has flagella all over its body which help it feed and move

Kingdom Fungi

• The oldest organism in the world is thought to be a fungus aged somewhere between 1500 - 10,000 years old
• All fungi are eukaryotic cells
• The cells of fungi:
  • Possess non-cellulose cell walls (often made of the polysaccharide chitin)
• Fungi are saprotrophs:
  • They obtain this energy and carbon by digesting dead/decaying matter extracellularly or from being parasites on living organisms
• Fungi reproduce using spores that disperse onto the ground nearby
• Fungi have a simple body form:
  • They can be unicellular (like the common baker’s yeast Saccharomyces cerevisiae)
  • Some consist of long threads called hyphae that grow from the main fungus body (mycelium)
  • Larger fungi possess fruiting bodies that release large numbers of spores
• Examples: moulds, yeasts, mushrooms

Kingdom Plantae

• Plants are multicellular eukaryotic organisms
• Plant cells:
  • All have cell walls composed of cellulose
  • Possess large (and usually permanent) vacuoles that provide structural support
  • Are able to differentiate into specialized cells to form tissues and organs
  • Possess chloroplasts (containing chlorophyll) that enable photosynthesis (not all plant cells have chloroplasts)
• They are autotrophs
  • This means they can synthesize their organic compounds and molecules for energy use and building biomass from inorganic compounds
• Examples: mosses, ferns, flowering plants

Kingdom Animalia

• Animals are also multicellular eukaryotic organisms
• Animal cells:
  • Are able to differentiate into many different specialised cell types that can form tissues and organs
  • Have small temporary vacuoles (for example, lysosomes)
  • Have no cell walls
• They are heterotrophs
  • They have a wide range of feeding mechanisms
• Examples: molluscs, insects, fish, reptiles, birds, mammals

The four kingdoms that fall under the domain Eukarya, representing the eukaryotes

• In the past, scientists encountered many difficulties when trying to determine the evolutionary relationships between species
• Using the physical features of species (such as colour/shape/size) has many limitations and can often lead to the wrong classification of species
• Advances in genome sequencing and immunology has allowed scientists to further investigate the evolutionary relationships between species
• This has led to many organisms being reclassified or changes being made to the classification system structure
• Scientific knowledge is constantly changing, as more technological advances are made
• One such example is the three domain classification system, which was based on new information obtained from molecular analysis of RNA genes in particular
  • Using this new information,scientists have realised that using cell type to classify organisms is insufficient, and that prokaryotes could be divided into two separate groups (domains)
  • The three domains are:
    • Archaea (prokaryotes)
    • Bacteria (prokaryotes)
    • Eukarya (eukaryotes)

The taxonomic classification system within the three domains

• This new classification system was based on molecular phylogeny
• Phylogeny investigates the evolutionary history of different groups of organisms and can specify how closely related they are
• Molecular phylogeny relies on similarities or differences of molecules (such as DNA, RNA or proteins) between groups of organisms to determine how closely related they are
• The more similar the molecules, the more recent the common ancestor is that they share
• Based on the evidence that molecular phylogeny provided, it was determined that the organisms in the kingdom Prokaryotae would be reclassified into two separate domains - the Archaea and Bacteria
• The evidence suggested that archaea and bacteria are less closely related to each other than scientists originally thought
• Organisms from the other four kingdoms where placed in another domain - Eukaryota

Characteristics & Features of the Three Domains Table