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Basic Unit of Life

Three Domains of Living Organisms

Scientists classify organisms partially based on cell type, with prokaryotes sorted into two domains, Bacteria and Archaea, and eukaryotes placed into their own domain.
Modern scientists classify all organisms into one of the three domains: Archaea, Bacteria, or Eukarya. A domain is the largest taxonomic grouping of organisms. The differences between types of cells have given biologists a framework for classifying living things and for understanding the relationships between different organisms. Early classifications were based on observations of physical similarities between organisms. Historically, the primary classification was between the groups Eukaryota and Prokaryota. This division was based on the presence or absence of a nucleus. Archaea and Bacteria were placed in the same group because they are prokaryotes. Modern technology has allowed a deeper understanding of additional structural and lifestyle differences between the Archaea and Bacteria. For example, the cell walls of these two groups are composed of different materials, and many Archaea are found in extreme environments. Now, scientists recognize that Archaea and Bacteria have little in common besides lacking a nucleus. Archaea have greater gene sequence similarity to Eukarya than to Bacteria. Modern classifications use comparisons of DNA sequences to establish the phylogenetic relationships between organisms.

Three Domains of Life

As a family tree shows how individual people are related to one another, a phylogenetic tree shows how genetically similar different groups of organisms (including the three domains) are to each other. Bacteria belong to the oldest group.
The prokaryotes are further divided into groups within the domains Archaea and Bacteria, but research is ongoing and a consensus hasn't been reached. Eukaryotes are divided into the kingdoms Plantae, Animalia, and Fungi and the group Protista. Protista includes single-celled and multicellular eukaryotes that do not fit the other three kingdoms. The group is not technically a kingdom because the organisms do not all descend from an ancestor that doesn't have descendents in other kingdoms. However, many scientists still refer to it as a kingdom out of convenience. Ongoing studies are improving general understanding of the evolutionary history of protists, and some scientists have suggested replacing all eukaryotic kingdoms with supergroups to better reflect their history. The organisms of the kingdoms Plantae, Fungi, and Animalia are sorted primarily by how they obtain their nutrition. Further levels of classification that become increasingly specific are used to group and name organisms. This system, the taxonomic hierarchy, includes domain, kingdom, phylum, class, order, family, genus, and species. The scientific name of an organism includes its genus and species names, italicized, with the initial letter of the genus name capitalized. (Note: In the study of plants and fungi, the word division is sometimes used as an alternative name for the taxonomic level phylum.) The organization of a phylogenetic tree depends on determining which organisms appear to share a common ancestor. As technology improves and new discoveries are made, the classifications are refined, so understanding the phylogenetic tree of life is a work in progress.

Classification of a Eukaryote and a Prokaryote

The classification of organisms begins with distinguishing a eukaryote (domain Eukarya) from a prokaryote (either domain Bacteria or Archaea). The levels of classification are, in order of specificity, domain, kingdom, phylum, class, order, family, genus, and species. The scientific name of an organism includes the genus and species.

Diversity of Prokaryotic Organisms

Prokaryotes, which include true bacteria and archaea, live in many different kinds of habitats.

A prokaryote is a unicellular organism with no nucleus. Prokaryotes are abundant and are thought to account for over half of the carbon contained in living organisms. They live in habitats ranging from Antarctic sea ice to the Negev desert, but the majority live in the soil, the subsoil, and ocean sediment. Some are able to move independently, often using a flagellum, a threadlike tail. Though some prokaryotes live together in colonies or attached in a group, they do not share the same level of connection and coordination as a multicellular organism. Animals provide habitats for prokaryotes both on their surfaces and internally. Humans have from 1,000 to 10,000 prokaryotes on every square centimeter of their skin and many more living inside their digestive systems. Prokaryotes are also found on plants, among roots and on bark and leaves. A relatively small number are floating in the atmosphere, where they have been detected at altitudes up to 77 km.

Bacteria can be difficult to distinguish from archaea. Bacteria describes prokaryotic, unicellular organisms containing a peptidoglycan (amino acid and carbohydrate) cell wall. Archaea encompasses prokaryotic, unicellular organisms whose cell membranes are different from the organisms in the Bacteria domain. Their cell walls lack peptidoglycan. The lipids (fatty acids) in the cell walls of bacteria and archaea are different. Some archaea, especially ones that thrive in environments of extreme heat, have a cell wall made of a lipid monolayer rather than a lipid bilayer. Archaea and bacteria have genetic differences, with archaea being more closely related to eukaryotes than to bacteria. Archaea also use different chemical reactions for metabolism.

Prokaryotes, as a group, have diverse mechanisms for obtaining energy and carbon, collectively known as metabolic processes. Some prokaryotic species are heterotrophs (organisms that obtain energy and carbon from consuming other organisms) and some are autotrophs (capable of making their own food). Autotrophic prokaryotes may be phototrophs or chemotrophs. A phototroph is an organism that obtains energy from the sun. A chemotroph is an organism that obtains energy through chemical reactions with certain organic or inorganic compounds, such as those containing sulfur.

The groups included within the domain Archaea are the Euryarchaeota, the Crenarchaeota, and the Korarchaeota. There is ongoing discussion about which taxonomic level to assign to these groups. Many of these organisms live in diverse and extreme environments. The Euryarchaeota contain salt-loving organisms (halophiles) and methane-producing organisms (methanogens) that were previously thought to be bacteria. Some Crenarchaeota are thermophiles, but others live in less extreme environments. Korarchaeota also include several varieties of thermophiles and are found in hot springs around the world.

The number of groups within the domain Bacteria is not yet known. Microbiologist Carl Woese, who first proposed the classification of organisms into the three domains, identified 12 bacterial phyla. These include the photosynthetic cyanobacteria, spirochetes with their distinctive spiral shape, several of which cause disease, and gram-positive bacteria, originally classified based on the ability of their cell wall to take up a violet dye. New groups continue to be discovered, as methods for sequencing and analyzing the DNA of bacteria improve, and some databases already list nearly 100.

Comparing Two Examples of Prokaryotes
Organism Escherichia coli Sulfolobus solfataricus
Domain Bacteria Archaea
Environment Many, including human lower intestines Volcanic hot springs
Optimal Growth temperature 37°C 75–80°C
Nutrition Heterotrophic (uses carbon sources from host) Lithoautotrophic (oxidizes sulfur) or chemoheterotrophic
Cell membrane Lipid bilayer with ester linkage Lipid monolayer with ether linkage
Shape Rod Irregular, sometimes lobed or spherical

The familiar E. coli bacterium and the extreme thermophilic S. solfataricus are examples of the extreme diversity of the prokaryotes.

Diversity of Eukaryotic Organisms

Some major eukaryotic groups include plants, which have cell walls and carry out photosynthesis; animals, which are multicellular and obtain nutrition by eating other organisms; and fungi, which may be single-celled or multicellular and digest food outside of their bodies.

The three true kingdoms of the eukaryotes include plants, animals, and fungi. These kingdoms are called “true” because the organisms that make them up all share similar structures, means of obtaining nutrients, forms of reproduction, and mechanisms of movement and/or interaction with their environment. Protists, which are single-celled eukaryotic organisms, are neither plant nor animal, and because they exist in such diverse and unique forms, they are given their own separate kingdom, Protista.

The kingdom Plantae consists of multicellular eukaryotes, which are autotrophs (organisms capable of making their own food). With few exceptions, plants are photosynthetic. They use a group of light-capturing pigments called chlorophylls to harness the sun's energy and use it to convert carbon dioxide and water into organic compounds. Chlorophyll is also responsible for giving plants their green appearance. Chlorophyll is usually found in leaf cells, in structures called chloroplasts. A chloroplast is a membrane-bound organelle found in plants and some other organisms that captures energy from light and converts it into chemical energy. Each plant cell is surrounded by a rigid carbohydrate-based cell wall, which offers protection but also limits the motility of the plant. Plants contain a fluid-filled organelle called a central vacuole that works with the cell wall to maintain the structure and rigidity of the plant. Although plants can make their own organic compounds through photosynthesis, they must also perform cellular respiration to convert organic compounds into cellular energy. Most plants live on land. While this means they must manage their water supply, it provides better access to sunlight and abundant carbon dioxide for photosynthesis. Most plants reproduce sexually, but many are also able to reproduce asexually.

Kingdom Animalia consists of heterotrophs that must obtain carbon and energy from consuming other organisms. They are unable to photosynthesize, but there are a few examples of animals that form a symbiotic relationship with photosynthetic organisms. All animals are multicellular, and most contain specialized tissues and organs. None have cell walls. Some animals are terrestrial, while others are aquatic. The simplest animals, sponges, lack symmetry, movement, and even true tissues. However, more recently evolved animals have body symmetry and are able to navigate their environment. Newer adaptations include the development of a nervous system, limbs, and an internal skeleton. Animal reproduction is mostly sexual, but some species are able to reproduce asexually.

Organisms in kingdom Fungi include eukaryotic organisms that may be unicellular or multicellular and that produce spores and contain chitin, a polysaccharide used for structure, in the cell walls. Most fungi live on land. Many fungi are decomposers that break down the wastes and dead materials of other organisms. Like animals, fungi are heterotrophic, meaning that they acquire energy by consuming other organisms. They lack an internal digestive system and instead digest their food extracellularly (outside of their bodies). They release digestive enzymes to break down food and then absorb the released nutrients. Like plants, the cells of fungi have cell walls. Most fungi reproduce both sexually and asexually. However, some reproduce using only one of these strategies.

Some eukaryotes do not fit neatly into any of the above categories. These diverse, mostly single-celled organisms are classified as protists. Some protists are plantlike and can photosynthesize, while others are heterotrophic, like animals and fungi. Animallike protists were historically called protozoans and were some of the first cells observed under a microscope. Most protists are aquatic. They are historically difficult to categorize because they are diverse in both characteristics and genetics. Some protists are parasitic, and some are free-living. Some protists reproduce asexually, while others reproduce sexually. Some protists, such as the one that causes malaria, have such complex life cycles that multiple different species of hosts are required to complete a single cycle.
Plants, animals, fungi, and protists belong to separate kingdoms within domain Eukarya. Plants are multicellular, have rigid cell walls, and can photosynthesize. Animals are multicellular, lack cell walls, and eat other organisms. Fungi are mostly multicellular, have cells walls, and digest food outside of their bodies. Protists are either unicellular or multicellular and can photosynthesize or eat other organisms.
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