You should have a working knowledge of the following terms:
Introduction and Goals
Bacteria are everywhere. They have been found at the deepest depths of the oceans and high above in the atmosphere. Based on sheer numbers and species diversity, they are the most successful group of life on the planet.
This tutorial is the first in a three-part series discussing prokaryotes. By the end of this first tutorial you should have a basic understanding of:
- The basic features of all prokaryotes
- The diverse lifestyles of prokaryotes
- Why prokaryotes can undergo rapid evolutionary change
- The different nutritional modes of prokaryotes
- The basic genetic organization of prokaryotes
- Asexual reproduction as a means for acquiring new genetic information
Figure 1. Colorized Image of a Bacterial Colony. (Click to enlarge)
A defining feature of prokaryotes is their lack of membrane-bound nuclei. This is not to say they lack subcellular specialization because some prokaryotes have very elaborate internal membranes. However, they generally have less subcellular specialization than eukaryotes (organisms with membrane-bound nuclei and organelles). Also, prokaryotes are usually much smaller than eukaryotic cells (1-5 microns compared to 10-100 microns). They are often described as single-celled organisms, but they can form colonies that show a remarkable level of complexity (as depicted in this colorized image of a bacterial colony). The shape of individual cells is used to classify prokaryotes; they can be either spherical (coccus), rod-shaped (bacillus), or helical (spirillum).
This animation is a simple game to test your understanding of the basic features of a prokaryote.
In the last few decades, several taxonomic schemes have been used to describe life. One of the simplest divided life into prokaryotes and eukaryotes; that is, those organisms without nuclei went into one group and those with nuclei went into another, respectively. Another commonly used scheme divided life into five kingdoms: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia. Keep in mind that classification schemes strive to show the evolutionary relationships between groups, and in recent years it has become apparent that the evolutionary relationships of prokaryotes are quite complex. One prokaryotic group, the Archaea, have some features that are more eukaryotic than prokaryotic. Although the Archaea lack a nucleus, their genetic organization is more like that of a eukaryote.
Figure 2. The Three-Domain System of Classification. (Click to enlarge)
To reconcile new data, the taxonomic scheme of life has been revised. The most current scheme proposes that life be divided into three domains. In this scheme prokaryotic organisms can belong to the domain Archaea or the domain Bacteria, while those organisms that have a nucleus comprise the third domain, Eukarya. Organisms that make up these three domains are sometimes referred to as archaebacteria, eubacteria and eukaryotes, respectively. This figure illustrates the relationship between the three domains. Keep in mind that the common ancestor of the prokaryotes most likely arose about 3 billion years ago.Archaea are sometimes referred to as extremophiles, inhabiting extreme environments (e.g., hot springs, salt ponds, Arctic ice, deep oil wells, acidic ponds that form near mines, and hydrothermal vents); however, these environments are not extreme to the archaea. In fact, many extremophiles die when moved to our environment. Life is relative.
The rest of the prokaryotes are classified as bacteria. Some textbooks and articles still refer to all prokaryotes as bacteria, but there is an increasing tendency to make a distinction between archaebacteria and bacteria.
Figure 3. Thermophilic (heat-loving) bacteria. (Click to enlarge). Limestone terraces, formed by precipitation from calcium-rich water flowing from a raised hotpool. Pink, green, and brown-colored archaebacteria occupy the thermal gradients in the flowing water (60-100°C).
Prokaryotes by the Numbers
In terms of metabolic impact and numbers, prokaryotes dominate the biosphere. They outnumber all eukaryotes combined. They live in a myriad of environments and even a teaspoon of common dirt can harbor 100 million or more bacteria. Not only are bacteria plentiful in total numbers, but the species diversity may be quite high as well. Although recognizing distinct species of bacteria is a challenge for microbiologists modern approaches using DNA diversity analysis, suggest that bacteria spawn new species quite rapidly. Recent studies suggest that in that same teaspoon of soil there could reside up to 1 million different species.
Fast Growth and High Rates of Evolution
In some cases, prokaryotes can divide in as little as 20 minutes (although much slower rates are also observed). Generally, prokaryotes have three factors that enable them to grow rapidly. First, prokaryotes have a small genome (genetic material). Second, prokaryotes have simple morphologies (structural features). Third, prokaryotes replicate via binary fission(cell division in which a prokaryotic chromosome replicates and the mother cell pinches in half to form two new daughter cells). These three factors allow for a short generation time. This short generation time means that evolutionary changes occur relatively quickly when compared to longer-lived species.
Genetic Organization Aids Fast Generation Times
Compared to eukaryotes, prokaryotes usually have much smaller genomes. On average, a eukaryotic cell has 1000 times more DNA than a prokaryote. This means that less DNA must be replicated with each division in prokaryotes.
The DNA in prokaryotes is concentrated in the nucleoid. The prokaryotic chromosome is a double-stranded DNA molecule arranged as a single large ring.
Prokaryotes often have smaller rings of extrachromosomal DNA termed plasmids. Most plasmids consist of only a few genes. Plasmids are not required for survival in most environments because the prokaryotic chromosome programs all of the cell's essential functions. However, plasmids may contain genes that provide resistance to antibiotics, metabolism of unusual nutrients, and other special functions. Plasmids replicate independently of the main chromosome, and many can be readily transferred between prokaryotic cells.
Prokaryotes replicate via binary fission. Binary fission is simply cell division whereby two identical offspring each receive a copy of the original, single, parental chromosome. Binary fission is a type of asexual reproduction (reproduction that does not require the union of two reproductive cells, and that produces offspring genetically identical to the parent cell). A population of rapidly growing prokaryotes can synthesize their DNA almost continuously, which aids in their fast generation times. Even as a cell is physically separating, its DNA can be replicating for the next round of cell division.
Figure 4. Binary division in a bacterium. (Click to enlarge)
This simple animation shows binary fission in a prokaryote.
Asexual Reproduction and the Transfer of Genetic Information Between Prokaryotes
Prokaryotes do not alternate between the haploid and diploid states, hence meiosis and fertilization are not components of their life cycles. (Note: Meiosis in eukaryotes leads to new combinations of genetic variation as a consequence of crossing over during the formation of eggs and sperm. Crossing over or recombination recombines or reorganizes allelic variation. Recombination can reorganize variation to separate less functional copies of genes from functional copies of genes.) Rather, binary fission is the main method of reproduction in prokaryotes. This form of asexual reproduction means that the genetic variation caused by the shuffling of genes that occurs during meiosis/fertilization does not occur in prokaryotes. Nonetheless, genetic variation does occur in prokaryotes, and mutations (coupled with short generation times) are one source of variation in the population. Remember that genetic variation, within a population, can be beneficial because it provides the raw materials for a population to adapt to a changing environment. Greater diversity in the gene pool increases the likelihood that at least some of the organisms in a population will have the right alleles to survive if environmental conditions change.
The occurrence of mutations can add beneficial variation to the genome, but many times these genetic changes can have negative consequences for the prokaryotic cell. The usual negative effect is to alter the function of the proteins that are encoded in genes. Over time, the prokaryotic population could accumulate a large number of these negative mutations lower the ability of the population to survive. This idea was called Muller's ratchet by J. Felsenstein after H. J. Muller who originally described the phenomenon (MULLER, H. J., 1964 The Relation of Recombination to Mutational Advance. Mutat Res 106: 2-9.; FELSENSTEIN, J., 1974 The evolutionary advantage of recombination. Genetics 78: 737-756.) The idea is that with each negative mutation that is accumulated in the genome, the prokaryote can not go back to the mutation-free state much like the click of a ratchet.
One way that genetic material can be moved between bacteria to potential repair negative mutations in the prokaryotic genome is transformation. Transformation occurs when prokaryotes acquire genes from their surrounding environment. This DNA might have been left behind by other bacteria (from the same or different species) when they died. The foreign DNA is directly taken up by the cell and expressed. If the DNA contains a beneficial gene (e.g., one encoding for antibiotic resistance), then the individuals harboring that gene will have a selective advantage over their non-transformed counterparts. As long as individuals with this gene reproduce more successfully, compared to those lacking the gene, they will be more fit and the gene will increase in frequency (i.e., microevolution, via natural selection, will occur). R.J. Redfield found that this form of recombination can overcome Muller's ratchet in a paper called "Evolution of bacterial transformation: is sex with dead cells ever better than no sex at all?" (REDFIELD, R. J., 1988 Genetics 119: 213-221.) In this case, sex is the result of genetic exchange due to transformation.
Other examples include transformation of nonpathogenic bacteria into pathogenic (harmful) strains. When harmless Streptococcus pneumoniae bacteria are placed in a medium containing dead cells of the pathogenic strain, they can take up the DNA from the dead pathogenic cells. If the formerly harmless bacteria pick up the gene for pathogenicity, they will become pathogenic themselves. It is important to point out that pathogenicity may not confer a long-term increase in fitness; if the host dies, the microsymbiont is left in a cold house.
Transformation is commonly used by genetic engineers to relocate bacterial genes.
Genetic material can also be moved between bacteria by conjugation. The mechanism of conjugation requires that two living prokaryotic cells physically join with one another. Typically DNA transfer only goes one way, with the "male" using an appendage called a pilus (plural, pili). In order to produce pili, prokaryotes must have a plasmid termed the F factor(fertility factor plasmid). When a cell has the F factor plasmid, it is said to be F+. This F+ condition is heritable. If an F+ cell divides, both of the resulting cells will be F+. This condition is also "contagious." After an F+ cell conjugates with a "female" cell that does not contain the F factor, the "female" cell obtains the F factor plasmid and becomes F+ ("male").
Click on the following to view a simple animation of an F-plasmid transfer.
Genetic material can also be moved between bacteria by transduction. In this event, the exchange of DNA between prokaryotes is made possible by phages(viruses that infect bacteria). Phages reproduce by injecting their genetic material inside the bacterial cell, then multiplying, and eventually bursting from the cell. In a mechanism referred to as specialized transduction, the phage DNA inserts somewhat benignly into the bacterial host chromosome. Here it can lay dormant for many generations. However, under certain conditions, the phage DNA excises itself from the bacterial chromosome (usually carrying pieces of the chromosome with it), then replicates and forms new phages that burst out of the cell. These phages can reinfect other bacteria and thereby transfer not only their own DNA, but pieces of the former host DNA into the newly infected bacterium.
Figure 5. Overview of Transduction. (Click to enlarge)
Genetic Variation and Evolution
The short generation time associated with binary fission was pointed out earlier in this tutorial. We also know that mutations add new and different alleles to populations. These two factors (short generation times and mutations), combined with the processes of transformation, conjugation,and transduction, help prokaryotic populations achieve vast genetic variation (without the alternation of haploid/diploid states seen in many eukaryotes). Generation times are minutes to hours, and can result in a beneficial mutation being heavily favored and passed on to a great number of offspring in a very short period of time. Once again, a short generation span enables prokaryotic populations to adapt very rapidly to environmental change. This adaptive evolution is as important now to prokaryotes as it was when prokaryotic life began to diversify a few billion years ago.
During the course of evolution, prokaryotes have adapted to a myriad of environments. Part of this adaptation involves different ways of obtaining energy and carbon. In looking at the diversity of prokaryotes, one observes many different nutritional modes. When considering nutritional modes, there are some general features that are commonly used to categorize the nutritional state of any life form.
All life can be categorized nutritionally, according to how an organism obtains its energy and from where it gets its carbon. The prefixes "chemo" and "photo" are used to describe whether the energy comes from a high-energy molecule (e.g., glucose) or from light, respectively. "Auto" and "hetero" are used to describe whether carbon dioxide or a more complex form of carbon is used as a carbon source, respectively. The prefixes are then affixed to the suffix "troph," meaning nourishment.
This tutorial introduced you to the prokaryotes. They are a very diverse group of organisms that are commonly referred to as bacteria; however, they are really comprised of two different domains. One domain, the Archaea, usually grow in the most extreme environments. Their ability to occupy extreme habitats is mirrored by their flexibility in utilizing resources; some species are photosynthetic, whereas others can live on oil or hydrogen sulfide. The other domain, the Bacteria, is much more abundant. Although diverse, members of both domains share some common features. Prokaryotes lack membrane-bound nuclei, they are generally single-celled or colonial, and they are very small. The genetic organization of prokaryotes and binary fission as a means for replication aids in their fast generation times, which contributes to relatively quick evolutionary changes. We will continue our discussion of prokaryotes in the next tutorial by exploring their morphologies and by describing some of their interactions with other life forms.