Biodiversity: The Three Domains of Life
January 14, 2004


Readings: Starr. Ch 18, pps 286-287.
If you are interested in reading more about the specific Kingdoms (but it is not required reading), Ch 20 covers Bacteria, viruses, and protists, Ch 21 Fungi, Ch 22 Plants, and Chs 23-24 cover invertebrates and vertebrates. The CD has a lot of information as well!


"The incredible diversity of life on this planet, most of which is microbial, is best understood in an evolutionary framework" -- Carl Woese, 2000

I. The Amazing Diversity and Unity Of Life: How Many Species Are There?

There are at least 5 million and perhaps 10 - 100 million species on Earth! (For a current list, see the Species 2000 website)

6 to 7 million in tropics alone
1.4 million species currently named and described
260,000 plant species, 50,000 vertebrate species (we are one), 1,200,000 insect species....

However, even with all this diversity.....all forms of life show unity in that they are all

Are based on the cell
Use the same genetic code (DNA and RNA)
Share similar or identical metabolic pathways and enzymes
Share similarities of cell structure

For example: 5 December 2002: The scientific journal Nature reports the DNA sequence of the Mouse Genome (a genome is a full complement of DNA contained in a cell). A big finding: despite the rather striking differences between mice and humans, over 99% of all mouse genes have a direct counterpart (or 'homologous gene') in humans...wow.

[Images of the Human Genome and Mouse Genome Issues of Nature]

Want more information? Read Human Biology by Proxy in the Mouse Genome Issue of Nature.


II. 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...we'll talk about this soon).

BUT
– the traditional 5 Kingdom system most of us learned in school says nothing about how organisms within Kingdoms or between kingdoms may be related to each other.


III. 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 single-celled 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! (It was there all along, we had just never thought to look for it!)

These unusual organisms were considered to be bacteria and named "archaebacteria" ('ancient' bacteria). They did not need sunlight or oxygen to grow, instead making all of their food from hydrogen sulfide and other chemicals spewing from the volcanic vents, living in a complex ecosystem with many other living organisms near the warm, mineral-rick waters of the vents. However, it soon became obvious from biochemical characteristics and DNA sequence analysis that there were numerous differences between these archaebacteria and other bacteria - too many differences to support the idea that there single-celled organisms were closely related to currently known bacteria. Before long, it was proposed that these archaebacteria were a completely separate "SuperKingdom" of single-celled life. 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. His publication: 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...).


IV. The Three domains - Some Characteristics:
Domain Archaea:
Life's Extremists...! Archaea are found in the harshest environments on Earth, and are the oldest known organisms on Earth, appearing in the fossil record over 3.6 BILLION years ago (3,600,000,000 years ago!)

1. Methanogens: the“methane-makers”
Use only CO
2, 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: the “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 60C (up to 110C 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!!!


Domain Bacteria: Domain Bacteria (or Eubacteria) is familiar to most people when associated with human or animal disease. However, most bacterial species do not (and cannot) cause disease. Most species even play beneficial roles for humans by producing antibiotics and food. The soil, and in fact all ecosystems on earth, teems with free-living bacteria that perform many essential functions in the biosphere, e.g. nitrogen fixation, decomposition of organic material, etc. Our bodies are covered with bacteria that make up our normal flora. We cannot even begin to estimate how many species of bacteria may exist on Earth, because the more we look, the more we find! [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 toxins 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]

Two major Divisions or Phyla:

1. Cyanobacteria: Photosynthetic ‘blue-green’ bacteria = produce O
2 gas. Photosynthetic bacteria first appeared in the fossil record 3.2 billion years ago, and completely changed Earth's environment from anaerobic (no free oxygen) to aerobic (containing oxygen gas) - these bacteria made the O2 rich atmosphere in which we live!!! These bacteria are very closely related to eukaryotic chloroplasts (more on this later). [Image]

2. Eubacteria: The "true bacteria". Examples: Enteric bacteria like E. coli, Salmonella typhus, Legionella, Heliobacter pylorii (cause of many ulcers), Neisseria gonorrhea (cause of gonorrhea), Nitrogen-fixing bacteria that are able to convert nitrogen gas into ammonia. Clostridium (tetanus, botulism). Bacteria within this division - proteobacteria - are very closely related to eukaryotic mitochondria (more on this later) and often move by whip-like flagella.

There are MANY more phyla of bacteria; To read more about bacteria we don't like, see the "Bad Bug Book".


Eukarya: 4 Kingdoms of Eukaryotes!

1. Protista – Single celled eukaryotes – Euglena, Amoeba, Paramecium etc. These single celled organisms with a nucleus are first seen in the fossil record 1.5 billion years ago.

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. Many 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 beer.

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 460 million years ago (mya), as bryophyes (mosses), with the first ferns appearing 410 mya, the first seed plants (gymnosperms) appearing 360 mya, and finally, the first flowering plants (angiosperms) appearing just 130 mya. 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 food—sugar, 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] Since we just want an overview, here is a REAL quick trip through time!

The first invertebrates appeared on Earth ~700 mya (sponges, jellyfish, corals), and about 550 mya, a period of rapid diversification of invertebrates, called the Cambrian Explosion, resulted in all the major body plans of animal life today.

The first chordates (and vertebrates, animals with backbones) appeared soon after:
520 mya: The first fish appear in the fossil record.
500 mya: The first crustaceans and molluscs appear
400 mya: First insects appear
350 mya: First amphibians appear
300 mya: First reptiles appear
230 mya: First dinosaurs appear
200 mya: First mammals appear
150 mya: First birds appear
60 mya: Early primates appear
10 mya: Hominids appear (Homo sapiens 500,000 years ago)

Special mention: Arthropods (includes insects):

"By nearly any measure, the most successful animals on the planet are the arthropods - from the king crab with its 12-foot armspan to microscopic insects and crustaceans. 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). [Quote]

And another special mention to Tetrapods (amphibians, reptiles, birds and mammals):

"Tetrapods were the first vertebrates to truly walk the land. Tetrapods are a name that we have given to anything with four feet (tetra=four, pod=feet). Before tetrapods existed, vertebrates (like fish) were all confined to living in aquatic habitats. The tetrapods began moving to land in the Paleozoic around 350 million years ago. [Quote]


Objectives:

1. Explain what is meant by the 'unity' and 'diversity' of life - give examples
2.
What are the names of the 3 Domains? Who is Carl Woese and what was his role developing the concept of 3 Domains?
3. Archaea:
Distinguish between the three groups. Why are thay called 'extremeophiles'?
4. Bacteria:
Distinguish between cyanobacteria and proteobacteria
5. Eukarya: Be able to list the 4 Kingdoms within Eukarya and give 1 representative organisms for each. Be able to describe when various vertebrates first appeared in the fossil record.