THE DIVERSITY OF LIFE
For many years the two-kingdom system of classification (animals and plants) prevailed, but was not suitable as biologists learned more about the structures and life histories of different organisms.
The five-kingdom system proposed by Robert H. Whittaker and modified by Lyn Margulis is still widely accepted today. These kingdoms include...
Kingdom Monera
Kingdom Protista
Kingdom Plantae
Kingdom Fungi, and
Kingdom Animalia
However these "kingdoms are not all "monophyletic" and considerable work is on going in an attempt to determine to more evolutionarily correct system.
Prokaryotes and the Origins of Metabolic Diversity
Prokaryotes include the heterotrophic Bacteria and the photoautotrphic Cyanobacteria. This is structurally and metabolically a very diverse group. It is thought that these are the earliest living organisms, having evolved about 3.5 billion years ago. From the fossil evidence they appear to have been the only forms of life for about 2 billion years. Prokaryotes are small and lack membrane bound organelles. Their name comes from "pro" = before, and "karyote" = nucleus. So these organisms lack a defined membrane bound nucleus. Most have cell walls but the composition and structure, differ from those cell walls found in plants, fungi and protists. Prokaryotes also differ from eukaryotes by having simpler genomes along with some differences in the mechanisms of genetic replication, protein synthesis and recombination. Prokaryotes are the most numerous organisms and can be found in all habitats.
These prokaryotes are very important to all other forms of life as decomposers and the key organisms in life-sustaining chemical cycles. We will discuss these ecological roles shortly. A small percentage of prokaryotes cause diseases in plants and animals. Many form symbiotic relationships with other prokaryotes and eukaryotes.
1. PROKARYOTIC FORM AND FUNCTION
A. The Morphology of Prokaryotes
Most prokaryotes are unicellular, or loosely colonial, some can have simple multicellular form such as a chain or filament, and some of the photosynthetic Cyanobacteria can even have a division of labour between specialised cells. Most have diameters of 1-5 mm (compared to eukaryotic diameters of 10-100 mm).
Bacterial cells have a diversity of shapes, the most common being spherical (cocci), rod-shaped (bacilli), and spiral (spirilla). Blue-green algae are often slightly larger than bacteria and can be unicellular, colonial or filamentous.
The above diagram is of a "Cyanobacteria" a bluegreen algae.
This is an example of the rod shaped "Bacillus"
These are the spherical "Cocci" bacteria.
These are the spiral shaped "spirillia" type of bacteria.
B. The Cell Surface
Prokaryotes have external cell walls that maintain the cell's shape. These cell walls also protect the cell, and prevents the cell from bursting in a hypo osmotic environment. These cell walls are different from the cell walls of the cell walls of the plants and fungi in that these prokaryotic cell walls are made of "peptidoglycan". Peptidoglycan is a modified sugar polymer cross-linked by short polypeptides. Exact composition of these polymers vary among species.
NOTE: Some antibiotics work by preventing formation of the cross-links in peptidoglycan, thus preventing formation of a function call wall.
One way microbiologists have developed to identify different species of bacteria is by the "Gram Stain". Gram stain a stain used to distinguish two groups of bacteria by virtue of a structural difference in their cell walls
"Gram positive bacteria" have simple cell walls with large amounts of peptidoglycan, therefore they stain blue. On the other hand "Gram negative bacteria", have more complex cells walls with smaller amounts of peptidoglycan, and an outer lipopolysaccharide-containing membrane that covers the cell wall. Because of these differences these bacteria stain pink with the gram stain. These gram-negative species are more often disease causing than are the gram-positive bacteria. The lipopolysaccharides in the cell's wall are often toxic, and the outer membrane helps protect these bacteria from host defence systems.
Many bacteria have other surface features, such as capsules and pili. A Capsule is a gelatinous secretion of some prokaryotes, which provides cells with additional protection, helps them adhere to hosts and helps form aggregates. Pili are surface appendages used for adherence to a host (in the case of a pathogen), or for transferring DNA when bacteria conjugate.
C. Motility of Prokaryotes
Motile bacteria use one of three mechanisms to move:
1. Flagella: These are filaments, composed of chains of the protein flagellin, are attached to another protein that forms a hook that is inserted into the basal apparatus. The flagellum spins around this basal apparatus in a circular motion, which is quite different from the motion of the eukaryotic flagella. Prokaryotic flagella are distributed on the cell surface or concentrated at one or both ends of the cell. Their rotation is powered by the diffusion of H+ into the cell. The H+ gradient is maintained by an ATP-driven proton pump.
2. Axial filaments of spirochetes allow rotation and a motion like a corkscrew.
3. Gliding along secreted slime.
Taxis is the movement towards or away from a stimulus. The stimulus can be light (phototactic), a chemical (chemotactic), or a magnetic field (magnetotactic). During taxis (directed movement), bacteria move by running and tumbling movements, enabled by rotation of flagella either counterclockwise or clockwise respectively. This causes flagella to move coordinately about each other (for a run), or to separate and randomize movements (for a tumble).
D. Internal Membranous Organization
Prokaryotes lack the diverse internal membranes characteristic of eukaryotes. Some prokaryotes, however, do have specialised membranes, formed by invaginations of the plasma membrane. The photosynthetic thylakoid membranes of Cyanobacteria are specialised membranes.
E. The Prokaryotic Genome
The prokaryotic genome has only 1/1000 as much DNA as the eukaryotic genome. The bacterial chromosome is called a "Genophore", and is usually one-double-stranded, circular DNA molecule. This DNA is concentrated in the nucleoid region, and is not surrounded by a membrane; therefore there is no true nucleus. The Genophore has very little protein associated with the DNA, unlike the eukaryotic chromosome which has a great deal of protein associated with it.
Many bacteria also have plasmids. Plasmids are smaller rings of DNA having supplemental (usually not essential) genes for functions such as antibiotic resistance or metabolism of unusual nutrients. These plasmids replicate independently of the chromosome, and can be transferred between partners during conjugation.
F. Growth, Reproduction, and Gene Exchange
Neither mitosis nor meiosis occur in the Monera. Instead reproduction is asexual and accomplished by binary fission. In bianary fission DNA synthesis is almost continuous, and cells can divide very rapidly. Growth (increase in number of cells) is geometric.
ie. (1 --> 2 --> 4 --> 8 --> 16 ...)
Generation time is usually 1-3 hours, although some can be as rapid as 20 minutes in optimal environments. At high concentrations of cells, growth slows due to accumulation of toxic wastes, lack of nourishment, etc. Under poor conditions Endospores, which are resistant cells, can be formed by some bacteria. An endospore contains one copy of the cell's chromosome surrounded by a thick wall. these resistant cells can survive adverse environmental conditions and toxins after the original cell disintegrates. Endospores may remain dormant for many years until proper environmental conditions return.
Although meiosis and syngamy do not occur in prokaryotes, genetic recombination can take place through three mechanisms...
1. Transformation is the process by which external DNA is incorporated by bacterial cells.
2. Conjugation is the direct transfer of genes from one bacterium to another.
Two bacteria "conjugating"
3. Transduction is the transfer of genes between bacteria by viruses.
Variable amounts of DNA are transferred by these mechanisms, leaving mutations as the major source of genetic variation in prokaryotes.
Metabolic diversity is greater in Monera than in all other kingdoms combined. Bacteria can be separated into four major groups depending on how they obtain energy and carbon.
1. Photoautotrophs need only light energy to synthesise ATP, and only need CO2 as a source of carbon in order to synthesise their organic compounds.
2. Photoheterotrophs must obtain their carbon in a more complex organic form but only need to use light energy to generate ATP.
3. Chemoautotrophs are organisms that need only CO2 as a carbon source and obtain energy by oxidizing inorganic compounds such as H2S, NH3 and Fe2+.
4. Chemoheterotrophs must obtain complex organic molecules as both a source of energy energy and as a source of carbon. Most bacteria are in this group.
The chemoheterotrophs can be broken down into subgroups: saprobes and parasites.
-Saprobes are decomposers that absorb nutrients from dead organic matter. They often excrete their digestive enzymes to the outside and then simply absorb the digested nutrients.
-Parasites are bacteria that absorb nutrients from body fluids of living hosts. These parasites like all parasites must therefore live inside the host.
The chemoheterotrophs are a very diverse group; some have very strict requirements while others are extremely versatile. Almost any molecule can serve as food from some species (e.g., some degrade petroleum and are used to clean oil spills). Those compounds that cannot be used by these organisms are considered non-biodegradable (e.g., some plastics).
Another way bacteria differ is in their response to oxygen. Obligate aerobes are bacteria that need O2 for cellular respiration. Facultative anaerobes are those bacteria that use O2 when present to improve their production of energy from glucose, but in the absence of oxygen they can grow by using the process of fermentation. Lastly there are the Obligate anaerobes which are those bacteria which are actually poisoned by O2 . These bacteria cannot grow at all in the presence of oxygen.
H. Prokaryotes and their roles in the Ecosystem
Prokaryotes are extremely important to the cycling of nutrients and important elements through ecosystems. One very good example is the "Nitrogen Cycle". Certain prokaryotes have the ability to "Fix" atmospheric nitrogen N2 into complex organic forms that are usable by other organisms. Nitrogen fixation (N2 into NH3) is unique to certain soil prokaryotes and Blue-green algae (Cyanobacteria) and is the only mechanism that makes atmospheric nitrogen available to organisms for incorporation into organic compounds. Some chemoautotrophic bacteria (Nitrosomonas sp.) can also convert ammonia (NH3) into a more reduced form nitrite NO2- and nitrate (NO3). Some facultative anaerobes such as Pseudomonas sp. can take the process the other way and "denitrify" NO2- or NO3- back into atmospheric N2. We will discuss these nutrient cycles in more detail in the next section of the course.
THE DIVERSITY OF PROKARYOTES
Due to ancient diversification and obscure fossil records, prokaryotic taxonomy has, until recently, been a classification of convenience in identification rather than reflecting the evolutionary relationships of this group. Recent advancements in molecular biology have allowed the development of "molecular systematics" which is the comparing of amino acid sequences of homologous proteins and base sequences of RNA and DNA in order to determine evolutionary relationships between groups of prokaryotes.
The use of molecular systematics (especially ribosomal RNA comparisons) have shown that prokaryotes split into at least two divergent lineages very early in their evolutionary development. These two lines are the archaea and the bacteria.
A. Archaea
These prokaryotes are interesting in that they live in some of the most inhospitable habitats on earth. Some characteristics of archaea include:
1. cell walls lack peptidoglycan,
2. plasma membranes that have a unique lipid composition,
3. and RNA polymerase and ribosomal proteins that are more like those of eukaryotes than of other bacteria.
Three Main Groups of Archaea
1. Methanogens
These bacteria use molecular hydrogen (H2) to reduce CO2 to methane (CH4). These bacteria are strict anaerobes, which cannot survive in the presence of oxygen. Some species are important decomposers in the mud in the bottom of marshes and swamps and form large amounts of methane or "marsh gas". Other species are important symbionts, which live inside certain protozoa which in turn live inside termites. Or these bacteria can also be found in the stomachs of herbivores such as cows.
2. Extreme halophiles
These are bacteria that live in waters of extreme salinity (15-20%). These bacteria survive the extreme hypertonic habitat by having a pigment bacteriorhodopsin in their plasma membrane, which absorbs light and uses the energy to pump H+ ions out of the cell. This pigment is also responsible for the pink colour of the colonies.
3. Thermoacidophiles
These bacteria live in very hot, acid habitats of 60-80 Co and pH 2-4, like the photo of a "Hot springs" below, the red stain on the rocks are the prokaryotic cells.
B. Bacteria
The major groups of eubacteria include a very diverse assemblage of organisms.
1. Actinomycetes
These bacteria are colonial with tubular branching hyphae that resemble those of the fungi. Reproduction is by fragmentation at the ends of the hyphae into spores. Most of the members of this group live in organic litter of soil. There are about 40 genera -- e.g., Streptomyces
2. Chemoautotrophic bacteria
These bacteria oxidize inorganic substances (e.g., NH3, H2S) for energy and use carbon from CO2 to synthesize organic molecules. Since O2 is the final electron acceptor these bacteria are obligate aerobes. They are commonly found in aerated soils. The group contains about 25 genera -- e.g., Nitrobacter.
3. Cyanobacteria (Blue-green algae)
These prokaryotes are photoautotrophs and use a photosynthesis mechanism that is just like that found in green plants and photosynthetic protista, splitting water and releasing O2. They contain the photosynthetic pigment chlorophyll a and two photosystems. The chlorophylls and electron-transport systems are embedded in thylakoid membranes, which run though out the cell cytoplasm. Phycobilins (accessory pigments) are also arranged in complexes on surface of thylakoids. The cell walls of this group are usually thick and gelatinous. The phylum contains many solitary, multi-cellular or colonial and filamentous genera. Motility is mostly by gliding. Most inhabit freshwater, some species are marine and many are found in moist soil or symbiotically associated with lichens.
Heterocysts are special cells found in some filamentous genera; these specialised cells contain the "nitrogen-fixing" enzyme complex. The group contains 32 genera -- example: Anabaena seen below.
Anabaena sp.
Gloeothecea sp.
4. Nitrogen-fixing aerobic bacteria
Both free-living and mutualistic species found in this group. The mutualistic species may be found in root nodules of legumes where they are important for proper plant nutrition. Along with the Cyanobacteria these nitrogen fixing bacteria contain the metabolic pathways which can "fix" atmospheric nitrogen N2 into reduced forms (nitrate, nitrite, and ammonia) that higher plants can use to make amino acids and therefore proteins. There are 5 genera -- e.g., Rhizobium sp.. The photograph below shows Rhizobium sp. in the root nodules of a bean plant.
THE IMPORTANCE OF PROKARYOTES
A. Prokaryotes and Chemical Cycles
Prokaryotes are critical links in the recycling of chemical elements between the biological and physical components of ecosystems.
Decomposers = bacteria that decompose dead organisms and waste of live organisms to return elements such as carbon and nitrogen to the environment in inorganic forms needed for reassimilation by other organisms, many of which are also bacteria.
Autotrophic bacteria = fix CO2, thus supporting food chains. Cyanobacteria supplement plants in restoring oxygen to the atmosphere as well as fixing nitrogen into nitrogenous compounds used by other organisms. Other prokaryotes also support cycling of nitrogen, sulphur, iron and hydrogen
B. Symbiotic Bacteria
Most prokaryotes form associations with other organisms; usually with other bacterial species possessing complementary metabolisms.
Symbiosis = ecological relationships between organisms of different species that are in direct contact. Usually the smaller organisms, the symbiont, lives within or on the larger host. Three categories of symbiosis:
Mutualism =symbiosis in which both partners benefit, for example, nitrogen-fixing bacteria in root nodules of certain plants fix nitrogen to be used by the plant, which in turn furnishes sugar and other nutrients to the bacteria.
Commensalism = symbiosis in which the symbiont benefits while neither helping nor harming the host.
Parasitism = symbiosis in which the symbiont (parasite) benefits at the expense of the host.
Symbiosis is believed to have played a major role not only in the evolution of prokaryotes, but also in the evolution of early protistans
Humans use bacteria for a variety of purposes. More than half of the antibiotics used to treat bacterial diseases come from cultures of various species of Streptomyces maintained by pharmaceutical companies. As simple models of life to learn about metabolism and molecular biology (E. coli is the best understood of all organisms).
Just some of the uses prokaryotes are put to:
- to digest organic wastes at sewage treatment plants.
- some species of pseudomonads are used to decompose pesticides and other synthetic compounds.
- to produce products that we can purify such as chemicals like acetone, vitamins and antibiotics and insulin. Genetic engineering has expanded these uses.
- to convert milk into yogurt and cheese.
Sewage treatment
Oil spill treatment.
