Kingdoms of Life

Prokaryotes: Bacteria and Archaea

Bacteria and Archaea

The two prokaryotic domains, Bacteria and Archaea, contain diverse single-celled organisms that exhibit a wide variety of metabolic abilities.
Although members of the domains (largest taxonomic groupings) Bacteria and Archaea have many important differences, they are united by their general cell type. Unlike members of the domain Eukarya, Bacteria and Archaea are prokaryotes. Prokaryotic cells lack a membrane-bound nucleus to contain the DNA, other membrane systems such as the endoplasmic reticulum, or membrane-bound organelles such as mitochondria, making them much smaller and simpler than eukaryotic cells. Prokaryotic organisms are all single-celled. 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. Prokaryotes carry their genes on a single circular chromosome, unprotected in the gel-like cytoplasm filling the interior of the cell. They may also carry some genetic material in plasmids. A plasmid is a small, circular piece of bacterial DNA that replicates on its own and can be transferred between cells. As single-celled organisms, their reproduction is equivalent to cell division. Prokaryotic cell division consists of replication of the single chromosome followed by a simple split of the cell, known as binary fission. Prokaryotes as a group have diverse mechanisms for obtaining energy and carbon, collectively known as metabolic processes. Some prokaryotes are phototrophs. 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. An autotroph is an organism that can make its own food. Autotrophs get their carbon from the atmosphere as carbon dioxide, or from other inorganic sources. A heterotroph is an organism that obtains energy and carbon from consuming other organisms. Heterotrophs obtain carbon from organic molecules. Bacteria can be described by combining their source of energy and their source of carbon. For example, a photosynthetic bacterium is considered a photoautotroph because it obtains its energy from the sun and its carbon from the atmosphere. There are prokaryotic species in each metabolic category.
There are multiple ways a unicellular organism called a prokaryote obtains carbon and energy. In general, an organism will first be categorized as either an autotroph or heterotroph. Autotrophs rely on carbon dioxide as their carbon source while heterotrophs rely on organic molecules as a carbon source. These organisms are further divided based on the method they use to get energy and carbon. Each method is used by at least one prokaryote.

Bacteria

Bacteria are small unicellular organisms that obtain food through a variety of processes.
The domain Bacteria is further classified into the kingdom Eubacteria and is the most diverse kingdom (second largest taxonomic grouping). It represents the greatest number of organisms, called by the generic term bacteria, although individuals in this kingdom are among the smallest of all life. They are so diverse that humans and potatoes are more closely related than many bacterial species are to each other. In addition to bacteria being metabolically diverse as a group, some individual bacteria are able to change metabolic strategies based on the environment. For example, some bacteria are able to use oxygen when it is present and switch to fermentation when oxygen is absent. Bacteria reproduce through simple cell division, but they can also exchange genetic material through conjugation. Conjugation involves the direct transfer of genetic material between two bacteria, using a small piece of DNA called a plasmid.

Although a relatively small proportion of pathogenic, or disease-causing, bacteria receives the most public attention, many bacteria perform critical ecological functions. Arguably the most important bacterial contribution to life on Earth was the transformation of the atmosphere by ancient photosynthetic cyanobacteria that made life possible for those organisms that require oxygen. However, bacteria still provide important ecological services.

All organisms require nitrogen for the formation of proteins. However, the nitrogen found in the atmosphere is not in a form that most living organisms can use. Some bacteria, called nitrogen-fixing bacteria, can convert atmospheric nitrogen into ammonia and other nitrogen-containing compounds. These compounds can then be used by plants, and subsequently animals, to supply their nitrogen needs. In this way, bacterial species are responsible for modifying atmospheric nitrogen to a form that eukaryotic organisms can use.

Bacteria function in the cycling of other elements through their role as decomposers. A decomposer is an organism that breaks down dead materials and organic wastes, releasing energy within an ecosystem. Bacteria break down these materials to release carbon, nitrogen, phosphorus, and other elements back into the ecosystem. Without the decomposing actions of bacteria and other organisms such as fungi, the supply of chemical elements in the environment would diminish and the continuity of life would cease.

A growing body of evidence has shown the importance of the microbiome, the types of organisms living in the human digestive tract. The specific organisms present, or absent, in the intestinal microbiome can play a role in obesity, diabetes, cardiovascular disease, and diseases of the digestive system. In addition, differences in intestinal microbiome can explain some nutritional deficiencies. Understanding the role of intestinal bacteria in health is a major area of research.

Major Groups of Bacteria

Gram staining is a method used to identify, based on cell wall structure, members of the different types of bacteria, such as Proteobacteria, Spirochetes, and Cyanobacteria.
Scientists use a method called a Gram stain to differentiate between types of bacteria based on cell wall structure. Developed in 1884 by Danish bacteriologist Hans Christian Gram, this staining method was originally developed to make bacteria more visible, not differentiate between variations. This method allows researchers to visualize the peptidoglycan layer found between the cell membrane and cell wall. Gram-positive cells have a thick layer of peptidoglycan that stains purple. Gram-negative cells have a thin layer of peptidoglycan and stain red. Gram-negative bacteria include Proteobacteria, Chlamydias, Spirochetes, and Cyanobacteria.
  • Proteobacteria are a diverse gram-negative group of bacteria that contain both oxygen-loving (aerobic) and oxygen-avoiding (anaerobic) species. Salmonella and E. coli are members of this group, as is the bacteria behind stomach ulcers.
  • Chlamydias are parasitic, requiring an animal host for survival. Their cell walls lack peptidoglycan, and one species from this group causes the human illness chlamydia.
  • Spirochetes move in a rotating spiral fashion with the help of a motile cell structure, the flagella. Not all are pathogenic, but Lyme disease is caused by a bacterium in this group.
  • Cyanobacteria are photoautotrophs that play an important role in the carbon cycle, converting carbon dioxide into organic compounds using energy from the sun. Ancient cyanobacteria were the evolutionary precursors of modern chloroplasts, the organelle involved in photosynthesis, and also helped to oxygenate the early Earth.
  • Gram-positive bacteria are responsible for strep infections, botulism, and anthrax.
Kingdom Eubacteria contains prokaryotic unicellular organisms. They can be found in just about every environment on Earth. They can be found in the water, in the air, and even in close association with animals, such as this koala. The bacteria live in the intestines of the koala and allow it to digest the leaves of eucalyptus.

Archaea

Archaea are prokaryotic organisms with a variety of structural and metabolic characteristics that distinguish them from bacteria.
The original classification of the Archaea was to place them within the kingdom Archaebacteria. While this classification scheme is not widely used anymore, it is still appropriate to include when comparing characteristics of all the kingdoms. This maintains consistency in the taxonomy and allows for six kingdoms instead of just five. This helps to further identify where these organisms sit in the hierarchy of life. Archaea share some characteristics with domain Bacteria, but genetic and other evidence indicates that archaea diverged from Bacteria a very long time ago. Archaea are currently thought to be more closely related to eukaryotes than to bacteria, their fellow prokaryotes. Archaea cells lack a nucleus or membrane-bound organelles, like bacterial cells. They also have a single circular chromosome. However, archaea cell walls do not have peptidoglycan, while bacterial cells do. Archaea also share some typically eukaryotic traits, many related to DNA. Like eukaryotes, some archaea have histones. A histone is a protein used to package DNA in condensed chromosomes. These proteins assist in DNA structure and control of gene expression. Archaea also have introns in some of their genes. An intron is a DNA sequence within a gene sequence that does not code for a specific protein; these must be removed from the mRNA during processing. This is a trait found in domain Eukarya but not in domain Bacteria. Archaea RNA polymerases (enzymes used to make mRNA) are also more similar to those of Eukarya than to those of domain Bacteria. Archaea have some unique traits that are not shared by any other domain. For example, many have lipids with branches in their cell membranes, while organisms of other domains have unbranched lipids in the cell membrane. This trait is thought to help stabilize membranes at high temperatures, as it is more common in heat-loving archaea. The members of Archaea gained reputations for being extremophiles. An extremophile is an organism that thrives in extreme conditions such as extreme salinity, pressure, chemical concentration, or temperature. This is partially because the first identified archaea were found under conditions that would not support most other life. For example, some archaea live in the very salty Great Salt Lake in Utah. Another example is the archaea that live near deep-sea hydrothermal vents. They thrive in very hot, high-pressure environments. Some archaea go beyond merely tolerating these extreme conditions and require them to survive. However, not all archaea live in such extreme conditions. For example, some reside in the human gut. A methanogen is an organism that uses carbon dioxide and hydrogen gas for energy. Methanogens release methane as a by-product. Among other functions, these archaea assist in digestion in some grass-eating animals, such as cattle. Oxygen is toxic to these archaea.
Archaea can be found in places where most other life cannot survive, such as under high-temperature, high-pressure conditions near deep-sea hydrothermal vents.