Bacteria and Archaea
[National Park Service Photo]
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|Prokaryotes can be found in every environment on earth. These microscopic creatures are everywhere from the polar ice caps to the hottest deserts. They can be found floating in water or recessed in the veins of a leaf. They are even on your own skin and inside animal digestive tracts. In fact, there are more prokaryotes in and on your body than the total number of humans who have ever lived. They are by far the most abundant organisms on earth. [Figure 17I-1: This relatively large eukaryotic cell (a rumen ciliate) is covered by prokaryotes (the small squiggles/rods). The small size of the majority of prokaryotes allows them to dominate the world in terms of numbers, without being noticed.].|
DESCRIPTION OF PROKARYOTES
The term "prokaryote" literally means "incompletely developed cells" from the Greek roots. This refers to the fact that prokaryotes lack a membrane-bound nucleus and organelles with membranes, which are features of eukaryotes, or "true cells". Instead of a nucleus, prokaryotes have a nucleoid region where the DNA is found. There are no mitochondria, chloroplasts, or other membrane-bound organelles in the cytoplasm, but there are ribosomes. [Figure 17I-2: Diagram of a "typical" prokaryotic cell]
In fact, most prokaryotes are about the same size as some organelles in eukaryotic cells. This fact has lent support to the idea that organelles such as mitochondria and chloroplasts evolved from bacteria that formerly existed as separate species living inside other cells. Examples of this situation exist today in corals and other organisms.
But not all prokaryotes are smaller than eukaryotes. The prokaryote called Epulopiscium fishelsoni, which lives in the gut of surgeonfish, is nearly a half-millimeter long -- 4-5 times longer than the large eukaryote Paramecium. Recently an even bigger prokaryote, Thiomargarita namibiensis, was found in the sediment off the coast of Namibia. In other words, small relative size is not a defining feature of prokaryotes, even though most are when compared to eukaryotes.
While there are no membrane-bound organelles in prokaryotes, there is, of course, a membrane that holds in the contents of the cell called the plasma membrane. As in all cells, the plasma membrane of prokaryotes is made of lipids. In prokaryotes that live in "normal" temperatures, the membrane is made of lipids similar to those of humans and other eukaryotes. In prokaryotes that live in high temperatures, such as some Archaea, the membrane is made of lipids with a higher melting point. The higher melting point results in the membrane having nearly the same fluidity at high temperatures as that of other organisms at lower temperatures. This is necessary so that the membrane can perform its function of regulating what goes into and out of the cell. Since prokaryotes do not have membranous organelles to perform functions like respiration and photosynthesis, the plasma membrane serves these purposes.
Outside of the plasma membrane, most prokaryotes have a relatively rigid cell wall for protection and support. In Bacteria, the cell wall is made of peptidoglycan, while Archaea have walls made of a variety of materials. Cell walls can be exposed directly to the environment or surrounded by a second lipid membrane. The fluid filling the space between the cell wall and the outer membrane is called periplasm The location of the cell wall and it's composition are important traits used in identifying prokaryotes.
Figure 17I-3 shows the two basic types of coverings, or cell envelopes, of Bacteria. In Bacteria, if a cell wall is exposed directly to the environment, it will react differently to dyes than a wall that is surrounded by an outer lipid membrane. If the cell envelope consists of only an inner plasma membrane and a thick outer cell wall exposed to the environment, the bacterium is called "Gram-positive." If the cell envelope consists of both an inner and outer lipid membrane sandwiching a thinner cell wall, the bacterium is called "Gram-negative". The term "Gram" is from the last name of the inventor of the process used to identify the type of cell envelope. Gram-positive bacteria turn purple after going through the process, called "Gram staining," while Gram-negative bacteria turn red. (Figure 17I-4) The Gram staining process has no effect on Archaea, since their cell walls are not made of peptidoglycan. Through any method, determining the type of cell wall is just one step in identifying prokaryotes.
Another trait used to identify prokaryotes is cell shape. There are three basic cell shapes (Figure 17I-5) : spherical cocci (top left), rod-shaped bacilli (top right) and spiral-shaped (bottom right). Each of these basic types can have modified forms, such as the vibrio shape in the lower left of Figure 17I-5. These individual cell shapes can exist independently or can be arranged into clusters or chains of two or more. Different species generally have specific cell shapes and tend to exist in particular arrangements. In addition to the basic shapes, prokaryotes can be filaments, stalked, irregular, square, or even star-shaped. Some can even change shape depending on environmental conditions.
The shape, along with the texture and color, of an entire colony of prokaryotes in a culture dish can be used in identification as well. Some form a smooth, round colony while others may form a lumpy colony with rough edges. Colonies can be whiteish, yellowish, reddish, etc. Figure 17I-6 shows bacterial colonies taken from the mouth (lower right) and the sole of a shoe (upper left). Notice the greater diversity of the colonies from the shoe. Not all prokaryotes can be grown in a culture dish to observe colonies, but if they can, the method is helpful in identification.
Many prokaryotes can be grown in a culture dish, but only in dishes made of specific media, or material. This fact provides another method of identifying. If a type of prokaryote needs a certain molecule to grow, that molecule must be present in the culture dish. Other times, a specific ingredient in a culture will inhibit the growth of some bacteria. In either case, if a prokaryote does or does not grow, the possible identification of the organism can be narrowed down.
Other environmental conditions, in addition to the culture medium, can be manipulated to help in identifying prokaryotes. Some can only grow in the absence of oxygen while others require it. Some need a specific range of temperature, pH, etc. Often times, one of the major distinguishing traits of an organism is the environment in which it lives.
One last trait used to identify prokaryotes is the organism's means of movement. Some move around by whipping their "tails," called flagella (Figure 17I-7), others glide along on a mucus trail, some adjust their bouyancy, some "corkscrew" through the environment, while others cannot move on their own power at all. Those that can move generally have a means to find desired things such as food or light, or to avoid undesirable things such as toxins. Many prokaryotes have receptors on their cell surface to detect substances or light and let the cell know which way to go. But it is the method and structures used for movement that are most easily observed for identification.
It is rare that any one trait can be used to identify a prokaryote. Usually, many traits are observed to conclude the identity of an organism. In plants and animals, there are many visible features which can be used in identification. Prokaryotes may be identified partially based on visible features, but often indirect observations are also needed. This section has not included an exhaustive list of methods used to identify prokaryotes, but it has given an idea of the variety of traits that may be used for that purpose.
Prokaryotes generally reproduce in a fairly straight-forward way through a process called binary fission. This is an asexual form of reproduction where a cell simply divides in two, yielding two distinct organisms. Each of the resulting cells has exactly the same DNA, so are called clones. Other prokaryotes reproduce by budding, a process where a smaller portion of the main cell pinches off and grows to full size (Figure 17I-8: Stalked Planctomyces budding.). The main way the genetic makeup of a population of prokaryotes changes is through mutation. Compared to sexual reproduction, this is a less efficient way of gaining genetic variablity. But once a favorable change takes place, the short generation times of prokaryotes allows the change to spread quickly.
While no known prokaryotes engage in true sexual reproduction, it is possible for some to exchange DNA through a process called conjugation. Figure 17I-9 shows a tube linking together two E. coli. DNA passes through this tube, and can contribute genes for resistance to antibiotics and other traits from one organisms to the other. Not all prokaryotes can do this, but for some it is a supplement to the variability provided by mutation.
The DNA of prokaryotes is typically a single, short, ring-shapedmolecule suspended in the cytoplasm, unassociated with proteins. This is in contrast to the many (46 in humans) longer, linear strands bound up by proteins in eukaryotes.
Note: Until recently, all known prokaryotes were thought to be bacteria, so the study of prokaryotes earned the name "bacteriology." Even though some prokaryotes are now placed in a completely different domain from bacteria, the term has stuck for the study of all prokaryotes.