Biodiversity: The Three Domains of Life
April 24, 2002
Web notes only!
"The incredible diversity of life on this planet, most of which is microbial, can only be understood in an evolutionary framework" -- Carl Woese, 2000
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.
(PS. Viruses are not in ANY of these kingdoms...remember that scientists do not classify them as 'alive').
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.
((We won't have time to go here...but what evidence do scientists have for how life began on planet Earth? Click lhere for last year's notes on "The Origin of Life" if you are interested!))
A New Proposal: The Three Domains of Life (Carl Woese, 1990)
Starting in the early 1970s, Dr. Carl Woese, a professor in the Department of Microbiology, University of Illinois, Urbana-Champaign, and other scientists began to find evidence for a previously unknown group of prokaryotic organisms. These organisms lived in extreme environments - deep sea hydrothermal vents, "black smokers", hot springs, the Dead Sea, acid lakes, salt evaporation ponds - environments that scientists had never suspected would contain a profusion of life!
Because they appeared prokaryotic, they were considered bacteria and named "archaebacteria" ('ancient' bacteria). However, became obvious from biochemical characteristics and DNA sequence analysis that there were numerous differences between these archaebacteria and other bacteria. Before long, it was realized that these archaebacteria were more closely related to the eukaryotes (including ourselves!) than to bacteria. Today, these bacteria have been renamed Archaea.
From this work, Dr. Woese proposed that there should be a new caterogy of classification of life - the Domain, a classification category above Kingdom. The Historic Paper: Woese, C.R., O. Kandler, & M.L. Wheelis (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya." Proc. Natl. Acad. Sci. USA 87:4576-4579. [Image]
PS. Carl Woese won the National Medal of Science in November 2000. Is there a Nobel prize in his future???? Dr. Marrs says YES! (Not that the Nobel Committee asks for my opinion...).
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 domains - Some
Bacteria: Domain Bacteria is familiar to most people when associated with human or animal disease. However, most bacterial species do not (and cannot) cause disease. Many species even play beneficial roles by producing antibiotics and food. The soil teems with free-living bacteria that perform many essential functions in the biosphere, e.g. nitrogen fixation. Our bodies are covered with bacteria that make up our normal flora. [Quote]
Fun Fact: There are more bacteria in one person's mouth than there are people in the world. Many are decomposers, some are photosynthesizers, and a few cause disease. Most bacteria cause disease by producing exotoxins that harm human cells, while others cause illness as a result of glycoproteins found on the outside of their capsules. There are many shapes that bacteria can come in, but three of the main ones are cocci (spherical), bacilli (rods) and spirochete (spiral bacteria). [Quote]
At least 5 major Phyla:
1. Proteobacteria: Enteric bacteria like E. coli, Salmonella typhus, Legionella, Heliobacter pylorii (cause of many ulcers), Neisseria gonorrhea (cause of gonorrhea). These bacteria are very closely related to eukaryotic mitochondria.
2. Cyanobacteria: Photosynthetic blue-green bacteria = produce O2 gas. Over 2 billion years ago, these bacteria made the O2 rich atmosphere in which we live!!! These bacteria are very closely related to eukaryotic chloroplasts. [Image]
3. Eubacteria: Clostridium (tetanus, botulism), Bacillus, mycoplasma (walking pneumonia).
4. Chlamydias: Parasites: Giardia, Chlamydia (STD)
5. Spirochaetes: Spiral bacteria: cause syphilis, Lyme disease
To read more about bacteria we don't like, see the "Bad Bug Book".
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. [Image]. 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 ive 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.
More Extremophiles here!!!
Extremophiles - Scientific American 1997 (PS. Written by Barry Marrs - but no relation!)
1. Protista Single celled eukaryotes Euglena, Amoeba, Paramecium etc
Protists can be found on land, in water, or
living inside other organisms. Some protists are photosynthetic,
like "phytoplankton", and produce more oxygen than all
land plants put together. Other protists are parasites or
predators. The protozoan Trypanosoma brucei
causes African Sleeping Sickness. This parasite it transmitted to
man by the bite of the tsetse fly. Another protozoan, Entameba
histolytica is a parasite of the stomach which
kills cells and drinks blood (but do not actually kill their
host). The protozoan Plasmodium vivax
causes malaria, carried by female mosquitos. Most protozoans move
by means of pseudopodia ("false feet") or by cilia
(little hairs). [Quote]
2. Fungi Mushrooms, bread molds, water molds, yeasts ,etc
The Kingdom Fungi includes some of the most important
organisms on Earth. By breaking down dead organic material, they
cycle nutrients through ecosystems. Other fungi provide drugs
such as penicillin and other antibiotics, foods like mushrooms,
truffles and morels, and the bubbles in bread, champagne, and
Fungi also cause plant and animal diseases: in humans, ringworm, athlete's foot, and several more serious diseases are caused by fungi. Plant diseases caused by fungi include rusts, smuts, and leaf, root, and stem rots, and may cause severe damage to crops. However, a number of fungi, in particular the yeasts, are important "model organisms" for studying problems in genetics and molecular biology. [Quote]
3. Plantae Flowering plants, gymnosperms (conifers), ferns, mosses, etc
Kingdom Plantae includes all land plants - an
amazing range of diverse forms with more than 250,000 species.
Plants first appeared on Earth in the Ordovician period
approximately 510 million years ago. The most striking, and
important, feature of plants is their green color, the result of a pigment called chlorophyll.
Plants use chlorophyll to capture light energy, which fuels the
manufacture of foodsugar, starch, and other carbohydrates. [Quote]
4. Animalia [There is so much to say about this Kingdom - please visit the links if you want more information!!!] [Image]
First appeared on Earth ~650 million years ago. Includes sponges, jellyfish, corals, fish (etc etc) and a special mention to: Arthropods (includes insects):
"By nearly any measure, the most
successful animals on the planet are the arthropods.
They make up over three-fourths of all currently known living and
fossil organisms, or over one million species in
all. Since many arthropod species remain undocumented or
undiscovered, the true number of living arthropod species is
probably in the tens of millions. One recent conservative
estimate puts the number of arthropod species in tropical forests
at 6 to 9 million species (Thomas, 1990).
"Arthropods range in distribution from the deep sea to mountain peaks, in size from the king crab with its 12-foot armspan to microscopic insects and crustaceans. Despite this unbelievable diversity, the basic body plan of arthropods is fairly constant. Arthropods have a stiff cuticle made largely of chitin and proteins, forming an exoskeleton. They have segmented bodies to form integrated units (heads, abdomens, and so on). The phylum takes its name from its distinctive jointed appendages, which may be modified in a number of ways to form antennae, mouthparts, and reproductive organs." [Quote]
And another special mention to Tetrapods (amphibians, reptiles, birds and mammals):
"Tetrapods were the first
vertebrates to truly walk the land. Before tetrapods existed,
vertebrates (like fish) were all confined to living in aquatic
habitats. The tetrapods began moving to land in the Paleozoic
around 360 million years ago. Tetrapods are a name that we have
given to anything with four feet (tetra=four, pod=feet).
Therefore all land dwelling vertebrates can be considered
tetrapods. Tetrapods, whose closest living relatives are
lungfish, have two main groups: amphibians and amniotes.
The amniotes in turn have two main groups: the synapsids
(including mammals) and the sauropsids
(including reptiles and their fossil relatives)." [Quote]
1. What are the names of the 3
Domains? Who is Carl Woese and what was his role developing the
concept of 3 Domains?
2. What is rRNA and why was did scientists choose it as an Evolutionary Chronometer?
3. Bacteria: What is the significance of the Proteobacteria and the Cyanobacteria in the development of eukaryotic organelles?
4. Archaea: Distinguish between the three groups. Why are thay called 'extremeophiles'?
5. Eukarya: Be able to list the 4 Kingdom within Eukarya and give 1 representative organisms for each. (You do not need to know dates, numbers of species, or other facts provided in the quotes).