Organizing the Diversity of Life

Living organisms show enormous diversity. Bacteria, mushrooms, oak trees, insects, whales, and humans may appear very different, but all are part of the biological world.

Scientists organize organisms into groups based on characteristics such as:

• Cell structure.
• Number of cells.
• Method of nutrition.
• Reproduction.
• Biochemistry.
• DNA and other molecular evidence.
• Evolutionary relationships.

At the broadest commonly used level of classification are the three domains of life:

Bacteria

Archaea

Eukarya

Domains contain extremely large groups of organisms. Within domains, organisms can be divided into smaller groups, including kingdoms.

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The Three Domains of Life

The three-domain system recognizes three major evolutionary lineages of cellular organisms:

• Domain Bacteria
• Domain Archaea
• Domain Eukarya

Bacteria and Archaea consist of prokaryotic organisms.

Eukarya contains eukaryotic organisms.

One of the most important first steps when classifying an organism is therefore determining whether its cells are prokaryotic or eukaryotic.

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Prokaryotic and Eukaryotic Cells

A prokaryotic cell does not contain a nucleus surrounded by a nuclear membrane.

Its DNA is located within the cell but is not enclosed inside a nucleus.

Prokaryotic cells also lack most membrane-bound organelles.

Bacteria and Archaea are prokaryotes.

A eukaryotic cell contains a membrane-bound nucleus.

Eukaryotic cells also contain membrane-bound organelles such as mitochondria.

Animals, plants, fungi, and diverse other eukaryotes belong to Domain Eukarya.

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Domain Bacteria

Bacteria are microscopic prokaryotic organisms.

Typical bacterial characteristics include:

• Usually unicellular.
• Prokaryotic cells.
• No membrane-bound nucleus.
• DNA located in a nucleoid region.
• No membrane-bound organelles.
• Usually reproduce by binary fission.
• Most possess cell walls containing peptidoglycan.

Bacteria occur almost everywhere on Earth.

They can be found in:

• Soil.
• Water.
• Air.
• Food.
• Oceans.
• Other organisms.
• The human body.

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Bacteria Are Extremely Diverse

Although bacteria have relatively simple cellular structures, they are extremely diverse.

Some bacteria:

• Carry out photosynthesis.
• Decompose dead organisms.
• Help digest food.
• Fix nitrogen.
• Cause disease.
• Produce useful chemicals.
• Live in association with other organisms.

Most bacteria are not harmful to humans.

Many are essential components of ecosystems.

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Bacterial Shapes

Bacteria occur in several common shapes.

These include:

• Cocci – approximately spherical.
• Bacilli – rod-shaped.
• Spirilla – spiral-shaped.

Shape can help identify bacteria, although modern classification uses many additional characteristics.

Scientists may also examine:

• DNA.
• Cell-wall chemistry.
• Metabolism.
• Biochemical reactions.

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Domain Archaea

Archaea are also prokaryotic organisms.

They were once grouped with bacteria because their cells appear superficially similar.

Both generally:

• Are unicellular.
• Lack a nucleus.
• Lack membrane-bound organelles.
• Have relatively small cells.

However, molecular evidence revealed important differences between Bacteria and Archaea.

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How Archaea Differ from Bacteria

Archaea differ from bacteria in important aspects of:

• Cell membrane chemistry.
• Cell-wall composition.
• DNA-associated proteins.
• Gene expression machinery.
• Ribosomal RNA sequences.

Unlike bacterial cell walls, archaeal cell walls do not contain peptidoglycan.

These molecular differences provide evidence that Bacteria and Archaea represent separate evolutionary lineages.

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Archaea and Extreme Environments

Some Archaea are extremophiles.

Extremophiles are organisms adapted to environmental conditions that would be difficult for many other organisms to tolerate.

Some Archaea live in:

• Very hot environments.
• Highly salty water.
• Acidic environments.
• Oxygen-free environments.

For example, some species live around hydrothermal environments or in extremely salty lakes.

However, it is incorrect to think that all Archaea live in extreme environments.

Archaea also occur in ordinary environments such as:

• Oceans.
• Soil.
• Wetlands.
• Animal digestive systems.

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Methanogens

Some Archaea are known as methanogens.

Methanogens produce methane as part of their metabolism.

They live in oxygen-poor environments such as:

• Wetlands.
• Sediments.
• Sewage systems.
• Digestive systems of some animals.

Methanogens play important roles in carbon cycling and methane production.

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Domain Eukarya

Eukarya contains all organisms composed of eukaryotic cells.

Eukaryotic cells contain:

• A membrane-bound nucleus.
• Mitochondria.
• A complex internal cytoskeleton.
• Other membrane-bound structures.

Eukaryotic organisms include both unicellular and multicellular forms.

Major groups traditionally discussed within Eukarya include:

• Animals.
• Plants.
• Fungi.
• Diverse protists.

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What Is a Kingdom?

A kingdom is a major classification group below domain.

The familiar hierarchy is:

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

Kingdoms group organisms that share important biological characteristics.

Historically, scientists used different numbers of kingdoms as classification systems developed.

This is important because there is not one permanently fixed kingdom system used identically by every modern biologist.

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Changing Kingdom Systems

Early classification systems recognized only a small number of kingdoms.

As scientists discovered microorganisms and learned more about cells, classification systems expanded.

DNA and molecular evidence later revealed relationships that could not easily be determined from appearance alone.

As a result, modern biological classification increasingly emphasizes evolutionary relationships, and some traditional kingdom categories have been revised.

For introductory biology, it remains useful to study major groups such as:

• Bacteria.
• Archaea.
• Animals.
• Plants.
• Fungi.
• Protists.

However, Bacteria and Archaea are domains, while Animalia, Plantae, and Fungi are well-established kingdoms within Eukarya.

"Protista" is often used in school-level classification, but modern evolutionary classification shows that the organisms traditionally grouped as protists do not form one single natural evolutionary group.

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Kingdom Animalia

Animalia contains animals.

General characteristics of animals include:

• Eukaryotic cells.
• Multicellular bodies.
• No cell walls.
• Heterotrophic nutrition.
• Specialized tissues in most groups.
• Ability to respond actively to the environment.

Animals obtain organic nutrients by consuming other organisms or organic material.

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Animal Diversity

Animalia includes organisms as different as:

• Sponges.
• Jellyfish.
• Worms.
• Insects.
• Mollusks.
• Fish.
• Amphibians.
• Reptiles.
• Birds.
• Mammals.

Despite their diversity, animals share important evolutionary and cellular characteristics.

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Kingdom Plantae

Plantae contains land plants and, depending on the classification framework, closely related photosynthetic lineages.

Typical plant characteristics include:

• Eukaryotic cells.
• Multicellular organization.
• Cell walls containing cellulose.
• Chloroplasts in photosynthetic tissues.
• Photosynthetic nutrition.

Plants use light energy to produce organic molecules through photosynthesis.

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Plant Diversity

Major groups of plants include:

• Mosses and related plants.
• Ferns and their relatives.
• Gymnosperms such as conifers.
• Angiosperms, or flowering plants.

Plants are essential to many ecosystems because they form the base of many food webs and release oxygen through photosynthesis.

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Kingdom Fungi

Fungi include organisms such as:

• Mushrooms.
• Molds.
• Yeasts.

Fungi are eukaryotes but differ significantly from both animals and plants.

Typical fungal characteristics include:

• Eukaryotic cells.
• Cell walls containing chitin.
• Heterotrophic nutrition.
• External digestion followed by absorption.
• Mostly multicellular organization, although yeasts are commonly unicellular.

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How Fungi Obtain Food

Fungi do not normally ingest food like animals.

Instead, many fungi:

• Release digestive enzymes into their surroundings.
• Break large organic molecules into smaller molecules.
• Absorb the resulting nutrients.

This makes fungi extremely important decomposers.

They recycle nutrients from dead organisms and organic waste back into ecosystems.

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Fungi Are Not Plants

Fungi were historically grouped with plants, but they are fundamentally different.

Plants generally:

• Have cellulose cell walls.
• Contain chloroplasts in photosynthetic tissues.
• Produce organic molecules through photosynthesis.

Fungi:

• Have chitin-containing cell walls.
• Do not have chloroplasts.
• Obtain organic nutrients from other sources.

Molecular evidence also confirms that fungi form a distinct evolutionary lineage.

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Protists

The term protist is traditionally used for diverse eukaryotic organisms that are not classified as animals, plants, or fungi.

Examples commonly described as protists include:

• Amoebas.
• Paramecia.
• Many algae.
• Various other unicellular and simple multicellular eukaryotes.

Protists show enormous diversity.

Some are:

• Photosynthetic.
• Heterotrophic.
• Unicellular.
• Multicellular.
• Motile.
• Non-motile.

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Why Protists Are Difficult to Classify

Traditional classification often placed organisms into Kingdom Protista if they were eukaryotes but did not fit clearly into Animalia, Plantae, or Fungi.

DNA evidence has shown that these organisms belong to many different evolutionary lineages.

Therefore, "protists" remain a useful descriptive term in introductory biology, but they should not be thought of as one simple, closely related evolutionary group.

This illustrates how biological classification changes as scientific evidence improves.

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Comparing Major Eukaryotic Groups

Animals, plants, and fungi are all eukaryotes.

They therefore share characteristics such as:

• Cells containing nuclei.
• Membrane-bound organelles.
• Mitochondria.

However, they differ in important ways.

Animals

• No cell wall.
• Heterotrophic.
• Usually obtain nutrients by ingestion.

Plants

• Cellulose cell walls.
• Usually photosynthetic.
• Chloroplasts in photosynthetic tissues.

Fungi

• Chitin cell walls.
• Heterotrophic.
• Obtain nutrients largely through external digestion and absorption.

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Worked Example: Classifying an Animal

Suppose an organism:

• Is multicellular.
• Has eukaryotic cells.
• Has no cell walls.
• Consumes other organisms.
• Has specialized tissues.

First, because it has eukaryotic cells:

Domain = Eukarya

Its other characteristics indicate:

Kingdom = Animalia

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Worked Example: Classifying a Plant

An organism:

• Is multicellular.
• Contains nuclei.
• Has cellulose cell walls.
• Contains chloroplasts.
• Carries out photosynthesis.

The presence of eukaryotic cells places it in:

Domain Eukarya

Its photosynthetic characteristics and cellulose-containing cell walls indicate:

Kingdom Plantae

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Worked Example: Classifying a Fungus

Scientists discover an organism that:

• Has eukaryotic cells.
• Has cell walls containing chitin.
• Does not contain chloroplasts.
• Releases digestive enzymes onto organic material.
• Absorbs the products of digestion.

Its domain is:

Eukarya

Its kingdom is:

Fungi

The chitin-containing cell wall and absorptive nutrition are particularly useful clues.

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Worked Example: Classifying a Bacterium

A microscopic organism:

• Consists of one cell.
• Has no nucleus.
• Has no membrane-bound organelles.
• Has a cell wall containing peptidoglycan.

Because it is prokaryotic, it cannot belong to Eukarya.

The presence of peptidoglycan supports classification in:

Domain Bacteria

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Worked Example: Classifying an Archaeon

Another microorganism:

• Is unicellular.
• Has no nucleus.
• Has no membrane-bound organelles.
• Does not have peptidoglycan in its cell wall.
• Has molecular characteristics typical of Archaea.

It belongs to:

Domain Archaea

This demonstrates why simply identifying an organism as a prokaryote is not enough to determine its domain.

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A Simple Classification Approach

When identifying an unknown organism, begin with its cells.

Does it have a membrane-bound nucleus?

If no:

It is a prokaryote.

Investigate whether molecular and biochemical evidence places it in:

Bacteria or Archaea

If yes:

It belongs to:

Eukarya

Then investigate characteristics such as:

• Cell walls.
• Chloroplasts.
• Number of cells.
• Nutrition.
• Reproduction.
• DNA.

These can help determine its more specific classification.

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Cell Walls Provide Useful Clues

Cell walls differ among major groups.

Bacteria

Most have cell walls containing peptidoglycan.

Archaea

May have cell walls, but they do not contain peptidoglycan.

Plants

Have cell walls containing cellulose.

Fungi

Have cell walls containing chitin.

Animals

Do not have cell walls.

These differences can provide important classification evidence.

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Nutrition Provides Useful Clues

How an organism obtains nutrients can also help classify it.

Plants

Usually produce organic molecules through photosynthesis.

Animals

Consume other organisms or organic material.

Fungi

Digest material externally and absorb nutrients.

Bacteria and Archaea

Show enormous metabolic diversity.

Some produce their own organic molecules, while others obtain them from other organisms or environmental sources.

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Comparing Bacteria and Archaea

Bacteria and Archaea have several similarities.

Both:

• Are prokaryotic.
• Are usually unicellular.
• Lack a membrane-bound nucleus.
• Lack most membrane-bound organelles.

However, they differ in important molecular and biochemical characteristics.

These differences are large enough that scientists classify them into separate domains.

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Comparing Prokaryotes and Eukaryotes

The distinction between prokaryotic and eukaryotic cells is one of the most important divisions in biology.

Prokaryotes:

• Lack a membrane-bound nucleus.
• Are generally smaller and structurally simpler.
• Include Bacteria and Archaea.

Eukaryotes:

• Have a membrane-bound nucleus.
• Have membrane-bound organelles.
• Include animals, plants, fungi, and diverse other groups.

However, "simpler" refers to cellular organization and does not mean prokaryotes are biologically unsuccessful or unevolved.

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Domains Reflect Evolutionary Relationships

The three-domain system was developed largely from molecular evidence.

Scientists compared molecules found in all cellular organisms, especially ribosomal RNA, or rRNA.

These comparisons revealed three major lineages:

Bacteria

Archaea

Eukarya

The three-domain system therefore represents more than differences in appearance.

It attempts to represent deep evolutionary relationships.

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Archaea and Eukarya

One particularly important discovery from molecular studies is that Archaea are not simply unusual bacteria.

Modern phylogenetic evidence shows a closer evolutionary relationship between Archaea and Eukarya than between either of those groups and Bacteria, although the detailed history of early cellular evolution is complex.

This demonstrates why molecular evidence is so important.

Two groups can appear structurally similar while having different evolutionary histories.

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Kingdoms Also Reflect Evolution

Kingdoms were originally based largely on visible characteristics.

Modern classification increasingly attempts to ensure that groups represent organisms sharing evolutionary ancestry.

Scientists therefore combine evidence from:

• DNA.
• RNA.
• Proteins.
• Cell structures.
• Anatomy.
• Development.
• Fossils.

As evidence changes, classification systems can also change.

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Classification Is Not a Ladder

The domains and kingdoms should not be imagined as a ladder from "simple" to "advanced."

Evolution produces a branching tree.

Bacteria are not organisms that failed to become eukaryotes.

Modern bacteria, archaea, animals, plants, fungi, and other organisms all belong to lineages that have continued evolving.

No living domain represents an earlier unfinished stage of another modern domain.

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Why Classification Systems Change

Classification systems are scientific models based on available evidence.

As new technologies become available, scientists obtain new information.

For example:

Microscopy

revealed cellular differences.

Biochemistry

revealed chemical differences.

DNA and RNA analysis

revealed evolutionary relationships.

Therefore:

new evidence → revised relationships → revised classification

Changing classification is part of normal scientific progress.

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Domains Versus Kingdoms

A common source of confusion is the difference between a domain and a kingdom.

A domain is broader.

A kingdom is below domain in the traditional taxonomic hierarchy.

For example:

Domain Eukarya

contains:

Kingdom Animalia

Kingdom Plantae

Kingdom Fungi

and several other eukaryotic lineages that may be treated differently in different classification systems.

Therefore:

Domain → Kingdom

not:

Kingdom → Domain

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Worked Comparison: Human and Mushroom

A human and a mushroom appear extremely different.

Human:

Domain: Eukarya

Kingdom: Animalia

Mushroom:

Domain: Eukarya

Kingdom: Fungi

They belong to different kingdoms but share the same domain.

This indicates that both possess eukaryotic cells despite their many other differences.

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Worked Comparison: Oak Tree and Human

Oak tree:

Domain: Eukarya

Kingdom: Plantae

Human:

Domain: Eukarya

Kingdom: Animalia

Both have eukaryotic cells.

However:

The oak has cellulose cell walls and photosynthetic tissues.

The human lacks cell walls and obtains organic nutrients through ingestion.

These differences help place them in different kingdoms.

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Worked Comparison: Bacterium and Human

A bacterium and a human belong to different domains.

Typical bacterium:

Domain: Bacteria

Human:

Domain: Eukarya

This represents a much broader classification difference than two organisms belonging to different kingdoms within the same domain.

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Using Several Characteristics Together

Scientists should not normally classify organisms using only one characteristic.

For example, being unicellular does not automatically mean an organism is a bacterium.

Some eukaryotes are unicellular.

Similarly, possessing a cell wall does not automatically mean an organism is a plant.

Cell walls also occur in:

• Bacteria.
• Archaea.
• Fungi.

Scientists therefore combine multiple characteristics and molecular evidence.

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Worked Classification Challenge

An unknown organism has:

• A nucleus.
• Mitochondria.
• Many cells.
• Cellulose cell walls.
• Chloroplasts.

Classification:

Domain Eukarya

because it has a nucleus and membrane-bound organelles.

Kingdom Plantae

because its characteristics include cellulose-containing cell walls and chloroplasts.

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Another Classification Challenge

An unknown organism has:

• No nucleus.
• No membrane-bound organelles.
• Peptidoglycan in its cell wall.

Classification:

Domain Bacteria

The lack of a nucleus identifies it as a prokaryote, while peptidoglycan provides strong evidence for Bacteria rather than Archaea.

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Another Classification Challenge

An organism has:

• A nucleus.
• Mitochondria.
• A chitin-containing cell wall.
• No chloroplasts.
• Absorptive nutrition.

Classification:

Domain Eukarya

Kingdom Fungi

Several characteristics support the classification rather than just one.

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Common Mistakes

Thinking Bacteria and Archaea Are the Same Group

Both are prokaryotic, but molecular evidence shows that they belong to separate domains.

Thinking All Archaea Live in Extreme Environments

Many Archaea live in ordinary environments.

Thinking All Bacteria Cause Disease

Most bacteria are not human pathogens, and many perform important ecological functions.

Thinking Fungi Are Plants

Fungi lack chloroplasts, have chitin-containing cell walls, and obtain nutrients differently from plants.

Thinking Every Unicellular Organism Is a Bacterium

Many eukaryotes are unicellular.

Thinking Every Organism With a Cell Wall Is a Plant

Bacteria, Archaea, and fungi can also possess cell walls.

Thinking Domain and Kingdom Are the Same Level

Domain is broader than kingdom.

Thinking "Protista" Represents One Simple Evolutionary Lineage

Traditional protists include many different eukaryotic lineages.

Thinking Classification Never Changes

Classification is revised as new evidence becomes available.

Thinking Domains Represent a Progression

The domains are branches of evolutionary history, not steps from primitive to advanced.

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Check Your Understanding

1. Name the three domains of life.

2. Which two domains contain prokaryotic organisms?

3. Which domain contains animals, plants, and fungi?

4. What is the major cellular difference between prokaryotes and eukaryotes?

5. Give three characteristics of bacteria.

6. Give two similarities between Bacteria and Archaea.

7. Give one important difference between Bacteria and Archaea.

8. Why is it incorrect to say that all Archaea are extremophiles?

9. What is a kingdom?

10. Give three major kingdoms within Eukarya.

11. Describe two characteristics of Animalia.

12. Describe two characteristics of Plantae.

13. Describe two characteristics of Fungi.

14. Why are fungi not classified as plants?

15. Why is the traditional group "Protista" difficult to fit into modern evolutionary classification?

16. An organism has eukaryotic cells, cellulose cell walls, and chloroplasts. Into which domain and kingdom would you classify it?

17. An organism lacks a nucleus and has peptidoglycan in its cell wall. Which domain does it belong to?

18. Why should scientists use several characteristics when classifying organisms?

19. How did molecular evidence contribute to the three-domain system?

20. Explain how domains and kingdoms can reflect evolutionary relationships.

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Key Terms

• Domain – broadest major taxonomic rank commonly used in biological classification.
• Kingdom – major classification rank below domain.
• Bacteria – domain containing prokaryotes with characteristic bacterial molecular and cellular features.
• Archaea – domain of prokaryotic organisms distinct from Bacteria in important molecular and biochemical characteristics.
• Eukarya – domain containing organisms with eukaryotic cells.
• Prokaryote – organism whose cells lack a membrane-bound nucleus.
• Eukaryote – organism whose cells contain a membrane-bound nucleus.
• Animalia – kingdom containing animals.
• Plantae – kingdom containing plants.
• Fungi – kingdom containing fungi.
• Protist – informal or traditional term for diverse eukaryotes outside animals, plants, and fungi.
• Peptidoglycan – major structural material in most bacterial cell walls.
• Cellulose – carbohydrate forming an important component of plant cell walls.
• Chitin – structural material found in fungal cell walls.
• Extremophile – organism adapted to environmental conditions extreme relative to those tolerated by many organisms.
• Phylogeny – evolutionary history and relationships among organisms.
• rRNA – ribosomal RNA, an important molecule used in studying evolutionary relationships.

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Key Takeaways

• Cellular life is commonly divided into three domains: Bacteria, Archaea, and Eukarya.
• Bacteria and Archaea are prokaryotic.
• Eukarya contains organisms with eukaryotic cells.
• Prokaryotic cells lack a membrane-bound nucleus.
• Eukaryotic cells contain a membrane-bound nucleus and membrane-bound organelles.
• Bacteria and Archaea may look similar at the cellular level but differ significantly in molecular and biochemical characteristics.
• Not all Archaea live in extreme environments.
• Major familiar kingdoms within Eukarya include Animalia, Plantae, and Fungi.
• Animals are multicellular heterotrophs without cell walls.
• Plants generally have cellulose cell walls and photosynthetic tissues containing chloroplasts.
• Fungi have chitin-containing cell walls and obtain nutrients largely through external digestion and absorption.
• Traditional "protists" represent a diverse collection of eukaryotic lineages rather than one simple evolutionary group.
• Cell walls differ among major groups and can provide useful classification evidence.
• Scientists use several characteristics together when classifying organisms.
• Modern classification relies heavily on DNA, RNA, and other molecular evidence.
• The three-domain system reflects major evolutionary relationships among organisms.
• Domain is a broader taxonomic level than kingdom.
• Classification systems can change when new evidence becomes available.
• Domains and kingdoms should be understood as parts of a branching evolutionary history, not as a ladder from simple to advanced.