Figure 14.15
. Prokaryote and eukaryote cells differ significantly in their structure. Unlike prokaryote cells (upper figure), eukaryote cells (middle figure, protist cell; lower figure, animal cell) have a nucleus, which is separated by membranes from the cytoplasm of the cell. Their organelles also have membranes. Herbert Copeland thought that these and other differences were significant enough to place prokaryote and eukaryote organisms in different superkingdoms.
In the 1920s, microbiologist Edouard Chatton gave bacteria the name prokaryotes. He defined prokaryote as an organism whose cells lack nuclei. He gave the name eukaryotes to all other organisms. He defined eukaryote as an organism whose cells have nuclei (see the Cell Structure and Function chapter). Chatton proposed placing prokaryotes and eukaryotes in a new taxon above the kingdom, called the superkingdom. However, this idea did not catch on, and most biologists continued to place bacteria in the protist kingdom.
Over the next several decades, scientists learned more about the tremendous number and diversity of bacteria. They started to see a need for a separate bacteria kingdom. By 1956, biologist Herbert Copeland proposed placing bacteria in a new kingdom called Monera. With the addition of the Monera kingdom, Linnaean taxonomy became a four-kingdom system (See Table below).
Bacteria are the most numerous organisms on Earth. In a single gram of soil, there are typically 40 million bacterial cells. The human body also contains 10 times as many bacterial cells as human cells. Most of these bacteria are on the skin or in the digestive tract.
The Fungi Kingdom
In the late 1960s, ecologist Robert Whittaker proposed adding a fifth kingdom to Linnaean taxonomy to represent fungi. Fungi are eukaryote organisms such as mushrooms and molds. Up until then, fungi had been classified in the plant kingdom. Whittaker separated fungi from plants on the basis of differences in metabolism. Plants make their own food in the process of photosynthesis, whereas fungi obtain nutrients by breaking down dead organisms (see the Fungi chapter). Separating fungi from plants resulted in five kingdoms, which are illustrated in Figure below. The five-kingdom system soon became widely accepted.
Figure 14.16
This five-kingdom system of classification was proposed by ecologist Robert Whittaker in the late 1960s. Whittaker added the Fungi kingdom to the earlier four-kingdom classification system.
Two Bacterial Kingdoms
By the 1970s, scientists had started to classify organisms in ways that reflected evolutionary relationships. They had also started using nucleic acid base sequences to identify these relationships (see Lesson 14.2). Nucleic acid sequence data are especially useful for studying bacteria. These organisms are so small that they have few physical traits.
Studies have bacterial nucleic acid sequences have yielded some surprising results. For example, in their research on ribosomal RNA base sequences, microbiologist Carl Woese and his colleagues discovered that bacteria actually include two very different groups of organisms. They called the two groups Eubacteria and Archaebacteria. Examples of organisms from each group are shown in Figure below. Although the two types of organisms are similar in appearance, their ribosomal RNA sequences are very different. In 1977, Woese and his colleagues suggested that the original bacteria kingdom should be divided into two new kingdoms, called Eubacteria and Archaebacteria. This resulted in a six-kingdom taxonomy that has been widely accepted for many years.
Figure 14.17
Left, Eubacteria (now called Bacteria), Right, Archaebacteria (now called Archaea). Appearances can be deceiving! These two microorganisms are very different from one another, despite their outward similarities. Both organisms used to be classified in the bacteria kingdom. Woese suggested placing them in different kingdoms, called the eubacteria and archaebacteria kingdoms.
Domains
Woese wasn’t completely happy with the six-kingdom system. It didn’t show that all four eukaryote kingdoms are more closely related to each other than to the two bacteria kingdoms. It also didn’t show that the two bacteria kingdoms are as different from each other as they are from the eukaryote kingdoms. To show these similarities and differences, Woese introduced a new taxon called the domain. He defined domain as a taxon higher than the kingdom.
The Three-Domain System
In 1990, Woese and his colleagues proposed a new classification system containing three domains: Bacteria, Archaea, and Eukarya. As shown in Figure below, the Bacteria domain was formerly the Eubacteria kingdom, and the Archaea domain was formerly the Archaebacteria kingdom. The Eukarya domain includes all four eukaryote kingdoms: plants, animals, protists, and fungi. The three-domain system emphasizes the similarities among eukaryotes and the differences among eukaryotes, bacteria, and archaea. By using domains, Woese was able to show these relationships without replacing the popular six-kingdom system.
Figure 14.18
This diagram shows how the three-domain system of classification is related to the six-kingdom system. Both Eubacteria and Archaebacteria kingdoms are raised to the level of domains (Bacteria and Archaea domains, respectively) in the three-domain system. The other four kingdoms make up the third domain (Eukarya domain).
Archaea were first found in extreme environments. For example, they were found in the hot water geysers in Yellowstone National park. Archaea have since been found in all of Earth’s habitats. They are now known to be present everywhere in high numbers. They may contribute as much as 20 percent to Earth’s total biomass.
Woese’s three-domain system was quickly adopted by many other biologists. There were some critics, however, who argued that the system put too much emphasis on the uniqueness of Archaea. Later studies confirmed how different Archaea are from other organisms. For example, organisms belogning to Archaea were found to differ from both Eukarya and Bacteria in the composition of their cell membranes and the system they use for DNA replication. These differences convinced most critics that the three-domain system was justified. After its introduction in 1990, the three-domain system became increasingly popular. Within a decade of its introduction, it had largely replaced earlier classifications.
How Are the Three Domains Related?
Comparing ribosomal RNA base sequences, Woese and his colleagues also showed that organisms belonging to Eukarya are more similar to Archaea than they are to Bacteria. Figure below is a phylogenetic tree based on their analysis. This tree places Archaea and Eukarya in the same clade (see Lesson 2). It represents the hypothesis that Archaea and Eukarya shared a more recent common ancestor with each other than with Bacteria.
Figure 14.19
This phylogenetic tree is based on comparisons of ribosomal RNA base sequences among living organisms. The tree divides all organisms into three domains: Bacteria, Archaea, and Eukarya. Humans and other animals belong to the Eukarya domain. From this tree, organisms that make up the domain Eukarya appear to have shared a more recent common ancestor with Archaea than Bacteria.
The results of a study published in 2007 seem to conflict with this hypothesis. Comparing DNA base sequences, the 2007 study suggested that the domain Archaea may be older than either Bacteria or Eukarya. That would make Archaea the most ancient group of organisms on Earth. It is not yet known, which, if either, hypothesis is correct. Scientists need to learn more about Archaea and their relationships with other organisms to resolve these questions.
The Future of Classification
The three-domain system is unlikely to be the final word on classification. The system is based on the current state of knowledge. As knowledge increases, the three-domain system may need revision. For example, the number of domains may change as scientists learn more about those life forms we currently know least about.
A recent discovery illustrates this point. In 2003, scientists identified a new virus called mimivirus. It resembles bacteria in size and number of genes. However, the virus cannot respond to stimuli or grow by cell division, both of which are traits of bacteria and other living organisms. Mimivirus’ unique
combination of traits seems to place it at the boundary between living and nonliving things. Some scientists think mimivirus might represent a new domain of life.
Lesson Summary
By 1977, four new kingdoms had been added to the plant and animal kingdoms of the original Linnaean taxonomy: Protista, Fungi, Eubacteria, and Archaebacteria.
In 1990, the three-domain system was introduced and is now the most widely used classification system. The three domains are Bacteria, Archaea, and Eukarya.
As knowledge of organisms increases in the future, the three-domain system may need revision. For example, new domains may need to be added.
Review Questions
Name four new kingdoms that were added to the original Linnaean taxonomy.
How do prokaryotes and eukaryotes differ?
Why were fungi placed in a separate kingdom from plants?
What is a domain?
Describe the relationship between the original bacteria kingdom called monera and the domain called bacteria.
Explain in which domain you would classify an organism that consists of a single cell with a nucleus.
Compare and contrast bacteria, Archaea, and Eukarya.
What problem with the six-kingdom classification system was addressed by the three-domain classification system? How did it address the problem?
Further Reading / Supplemental Links
Olaf Breidbach, Visions of Nature: The Art and Science of Ernst Haeckel. Prestel Publishing, 2006.
John L. Howland, The Surprising Archaea: Discovering Another Domain of Life. Oxford University Press, 2000.
Oladele Ogunseitan, Microbial Diversity: Form and Function in Prokaryotes. Wiley-Blackwell, 2004.
Vocabulary
archaea
Domain that was formerly the Archaebacteria kingdom.
bacteria
Domain that was formerly the Eubacteria kingdom.
domain
Taxon higher than the kingdom.
eukarya
Domain that includes all four eukaryote kingdoms: plants, animals, protists, and fungi.
eukaryote
Organisms whose cells have nuclei.
fungi
Kingdom of eukaryote organisms such as mushrooms and molds.
monera
Original name of the kingdom that included all bacteria.
prokaryote
Organism whose cells lack nuclei.
protista
Kingdom of single-celled, eukaryote organisms such as protozoa, often called “protists.”
Points to Consider
Robert Whittaker separated the fungi from the plant kingdom on the basis of their different ways of obtaining energy. You might expect Whittaker to focus on this type of difference because he was an ecologist.
What do you think ecology is?
What do you think ecologists study?
In addition to ways of obtaining energy, what traits of organisms do you think ecologists are likely to be most interested in?
Chapter 15: Principles of Ecology
Lesson 15.1: The Science of Ecology
Lesson Objectives
State what ecologists study, and identify levels of organization in ecology.
Define ecosystem, niche, and habitat, and explain how the concepts are related.
Describe methods of ecology, such as field studies, sampling, statistical analysis, and modeling.
Introduction
Ecology is the scientific study of the interactions of living things with each other and their relationships with the environment. Ecology is usually considered to be a major branch of biology. However, ecology has a more broad scope, because it includes both organisms and their environments. Examining the interactions between organisms and the environment can provide a basic understanding of the richness of life on earth and can help us understand how to protect that richness, which is increasingly threatened by human activity. Regardless of the challenges associated with conducting research in natural environments, ecologists often carry out field experiments to test their hypotheses.
Organisms and the Environment
Ecology is guided by a number of basic principles. One principle is that each living organism has a continual relationship with every other element in its environment. In this context, the environment includes both living and nonliving components.
Organisms
An organism is a life form consisting of one or more cells. All organisms have properties of life, including the ability to grow and reproduce. These properties of life require energy and materials from the environment. Therefore, an organism is not a closed system. Individual organisms depend on and are influenced by the environment.
The Environment
To the ecologist, the environment of an organism includes both physical aspects and other organisms. These two components of the environment are called abiotic and biotic components, respectively.
Abiotic components, or abiotic factors, are the non-living physical aspects of the environment. Examples include sunlight, soil, temperature, wind, water, and air.
Biotic components, or biotic factors, are the living organisms in the environment. They include organisms of the same and different species.
Biotic components can be very important environmental influences on organisms. For example, the first photosynthetic life forms on Earth produced oxygen, which led to the development of an oxygen-rich atmosphere (see the History of Life Chapter). This change in Earth’s atmosphere, in turn, caused the extinction of many life forms for which oxygen was toxic and the evolution of many other life forms for which oxygen was necessary.
Levels of Organization
Ecologists study organisms and their environments at different levels. The most inclusive level is the biosphere. The biosphere consists of all the organisms on planet Earth and the areas where they live. It occurs in a very thin layer of the planet, extending from about 11,000 meters below sea level to 15,000 meters above sea level. An image of the biosphere is shown in Figure below. Different colors on the map indicate the numbers of food-producing organisms in different parts of the biosphere. Ecological issues that might be investigated at the biosphere level include ocean pollution, air pollution, and global climate change.
Figure 15.1
This image of Earths surface shows the density of the chief life forms that produce food for other organisms in the biosphere. Plants are the chief food producers on land, and phytoplankton are the chief food producers in the ocean. The map shows the density of plants with a measure called the normalized difference vegetation index and the density of phytoplankton with the chlorophyll concentration.
Ecologists also study organisms and their environments at the population level. A population consists of organisms of the same species that live in the same area and interact with one another. You will read more about populations in the Populations chapter. Important ecological issues at the population level include:
rapid growth of the human population, which has led to overpopulation and environmental damage;
rapid decline in populations of many nonhuman species, which has led to the extinction of numerous species.
Another level at which ecologists study organisms and their environments is the community level. A community consists of populations of different species that live in the same area and interact with one another. For example, populations of coyotes and rabbits might interact in a grassland community. Coyotes hunt down and eat rabbits for food, so the two species have a predator-prey relationship. Ecological issues at the community level include how changes in the size of one population affect other populations. The Populations chapter discusses population interactions in communities in detail.
Ecosystem
A community can also be defined as the biotic component of an ecosystem. An ecosystem is a natural unit consisting of all the living organisms in an area functioning together with all the nonliving physical factors of the environment. The concept of an ecosystem ca
n apply to units of different sizes. For example, a large body of fresh water could be considered an ecosystem, and so could a small piece of dead wood. Both contain a community of species that interact with one another and with the abiotic components of their environment. Another example of an ecosystem is a desert, like the one shown in Figure below.
Figure 15.2
This desert ecosystem in southern California has fewer species than most other types of ecosystems, but it is still home to a community of interacting species (such as the cacti and grasses shown here) and potent environmental factors such as extreme heat and dryness.
Like most natural systems, ecosystems are not closed, at least not in terms of energy. Ecosystems depend on continuous inputs of energy from outside the system. Most ecosystems obtain energy from sunlight. Some obtain energy from chemical compounds. In Lesson 2, you will read how energy is transferred in ecosystems. In contrast to energy, matter is recycled in ecosystems. Elements such as carbon and nitrogen, which are needed by living organisms, are used over and over again. You will read how elements and water are recycled through ecosystems in Lesson 3.
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