How is Life Classified?

Before 1969: Life was classified into two kingdoms: Plant Kindgom Animal Kingdom
From 1969 1990: Life was classified into 5 Kingdoms: Monera, Protista, Plantae, Fungi,
Animalia, by R.H. Whittaker [Science 163, 150 (1969)] using classification according to
Linnaeus based on anatomy, morphology, embryology, and cell structure.

BUT the traditional 5 Kingdom system says nothing about how organisms within Kingdoms or
between kingdoms may be related to each other via evolutionary relationships among the
kingdoms.

A New Proposal: The Three Domains of Life (Carl Woese, 1990)

How was the 'Three Domain' Classification of Life Determined?
Woese (and many other scientists involved in this project) used the nucleotide sequence
of Ribosomal rRNA (the small subunit) and other RNA and protein sequences as an
Evolutionary Chronometer an evolutionary time clock.
What makes rRNA (or another sequence) a good chronometer?
1. It is universally distributed across group chosen all organisms have rRNA
2. It is functionaly similar between organisms rRNAs all participate in protein synthesis
3. Its sequence changes slowly - good for looking across long periods of time
4. The rRNA sequences can be aligned, or matched up, between 2 organisms
Other sequences that can be used are the large rRNA subunit, or the gene for cytochrome c
oxidase, ferredoxin.

The Three Domain System

As scientists learn more about organisms, classification systems change. Genetic sequencing has
given researchers a whole new way of analyzing relationships between organisms.
The current system, the Three Domain System, groups organisms primarily based on differences
in ribosomal RNA structure.
Ribosomal RNA is a molecular building block for ribosomes.
Under this system, organisms are classified into three domains and six kingdoms. The domains
are Archaea, Bacteria, and Eukarya. The kingdoms are Archaebacteria (ancient bacteria),
Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia.
The Archaea and Bacteria domains contain prokaryotic organisms. These are organisms that do
not have a membrane bound nucleus.

Eubacteria are classified under the Bacteria domain and archaebacteria are classified as
Archaeans.
The Eukarya domain includes eukaryotes, or organisms that have a membrane bound nucleus.
This domain is further subdivided into the kingdoms Protista, Fungi, Plantae, and Animalia.

The Three domains - Some Characteristics:

Domain Archaea prokaryotic, no nuclear membrane, distinct biochemistry and RNA markers

from bacteria, possess unique ancient evolutionary history for which they are considered some of
the oldest species of organisms on Earth; traditionally classified as archaebacteria; often
characterized by living in extreme environments. Some examples of archaeal organisms
are methanogens which produce the gas methane, halophiles which live in very salty water,
and thermoacidophiles which thrive in acidic high temperature water.

Archaea: Life's Extremists...!

1. Methanogens: methane-makers
Use only CO2, H and N to produce energy to live, and as a result give off methane gas. Live in
swamps, marshes, gut of cattle, termites, etc. Methanococcus jannaschii, isolated from the deep
sea Alvin probe, was the first Archaean whose genome was sequenced. Methanogens are
decomposers; and can be used in sewage treatment. Methanogens may someday be used to
produce methane as fuel!
2. Extreme Halophiles: salt lovers
Require an environment as salty or even10x saltier than ocean water. Some prefer up to 30% salt
concentrations! These bacteria live in the Dead Sea, the Great Salt Lake, salt evaporation ponds.
3. Extreme Thermophiles: heat / cold lovers
Prefer temperatures above 60 C (up to 110 C for hyperthermophiles!) or near or below
freezing. (Some thermophiles will die at roon temperature).
Thermophiles live in hot sulfur springs, Yellowstone Park, deep sea hydrothermal vents black
smokers, geothermal power plants. Also live in ocean waters around Antarctica, under the polar
ice caps, etc. Thermus aquaticus and Pyrococcus furiosis and two species.
Domain Bacteria prokaryotic, consists of prokaryotic cells possessing primarily diacyl
glycerol diester lipids in their membranes and bacterial rRNA, no nuclear membrane,
traditionally classified as bacteria. Most of the known pathogenic prokaryotic organisms belong
to bacteria and are currently studied more extensively than Archaea. Some examples of bacteria
include Cyanobacteria photosynthesizing bacteria that are related to the chloroplasts of
eukaryotic plants and algae, Spirochaetes Gram-negative bacteria that include those causing

syphilis and Lyme disease, and Firmicutes Gram-positive bacteria including Bifidobacterium
animalis which is present in the human large intestine.
Domain Eukarya eukaryotes, organisms that contain a membrane bound nucleus. An
inexhaustive list of eukaryotic organisms includes:

Kingdom Fungi or fungi

Examples:

Saccharomycotina includes true yeasts

Basidiomycota includes blue oyster mushrooms

Kingdom Plantae or plants

Examples:

Bryophyta mosses

Magnoliophyta flowering plants

Kingdom Animalia or animals

Examples:

Arthropoda includes insects, arachnids, and crustaceans

Chordata includes vertebrates and, as such, human beings

Comparison of Classification Systems

Five Kingdom System
Kingdoms: Monera, Protista, Fungi, Plantae, and Animalia.

Three Domain System

Archaea Domain
Archaebacteria Kingdom

Bacteria Domain
Eubacteria Kingdom
Eukarya Domain

Protista Kingdom

Fungi Kingdom

Plantae Kingdom

Animalia Kingdom
As we have seen, systems for classifying organisms change with new discoveries made over
time. The earliest systems recognized only two kingdoms (plant and animal).
The current Three Domain System is the best organizational system we have now, but as new
information is gained, a different system for classifying organisms may later be developed.