BIOLOGY ANIMAL

BIOLOGICAL DIVERSITY: BACTERIA AND ARCHAEANS
Table of Contents
Traditional classifications have placed the archea and bacteria into a single taxonomic kingdom due to theri morphological similarity. In fact the two groups are extremely different, as different from each other biochemically as eukaryotes are from either group. Under the recently devised domain system, the achaea and bacteria are placed into two separate domains, with the third one containing all the eukaryotes. This system is shown in Figure 1.




Domain Bacteria (Eubacteria) |
The old taxonomic Kingdom Monera consisted of the bacteria (meaning the true bacteria and cyanobacteria, or photosynthetic bacteria) as well as the archea. The modern classification, see Figure 1, seprates each of these groups to separate domain status.

Organisms in the Domain Bacteria lack membrane-bound organelles such as the nucleus and endoplasmic reticulum that typify the third domain, the Eukaryota. All members of Domain bacteria are prokaryotes. Bacteria (technically the Eubacteria) and blue-green bacteria (the blue-green algae when I was a student back in the 1970s), or cyanobacteria are the major forms of life in this domain, examples of which are shown in Figure 2.

Their small size, ability to rapidly reproduce (for example, the intestinal bacterium E. coli can reproduce by binary fission every 15 minutes), and diverse habitats/modes of existence make bacteria the most abundant and diversified group of organisms on (and under!) the Earth. Bacteria occur in almost every environment on Earth, from the bottom of the ocean floor, deep inside solid rock, to the cooling jackets of nuclear reactors. Possible bacteria-like structures have even been recovered from 3 billion year old Martian meteorites. If these turn out to be fossils (and as of 2002 it seems likely they are NOT), then the bacterial form of life would have existed simultaneously on both Earth and Mars. However, the cellular nature of the Martian structures has not been conclusively established.

Bacterial Structure |
Bacteria, since they are prokaryotes, lack a nuclear membrane and membrane-bound organelles. Biochemical processes that normally occur in a choloroplast or mitochondrion of eukaryotes will take place in the cytoplasm of prokaryotes. Bacterial DNA is circular and arrayed in a region of the cell known as the nucleoid, shown in Figure 3. Scattered within bacterial cytoplasm are numerous small loops of DNA known as plasmids. Bacterial genes are organized in by gene systems known as operons. The cytoplasm also contains numerous ribosomes, the structures where proteins are assembled. All bacteria also have a cell membrane, as well as a cell wall, as shown in Figure 4.

As a group, bacteria are nutritionally quite diverse. Some bacteria are photosynthetic autotrophs, while others are heterotrophs. Bacteria play important ecological roles as decomposers, as well as important elements of phytoplantonic organisms at the base of many food chains.

Plasmids are small DNA fragments known from almost all bacterial cells. These plasmids may carry between two and thirty genes. Some plasmids seem to have the ability to move in and out of the bacterial chromosome. As such they are important tools to the biotechnology arsenal.

The operon model of prokaryotic gene regulation was proposed by Fancois Jacob and Jacques Monod. Groups of genes coding for related proteins are arranged in units known as operons, as illustrated by Figure 5. An operon consists of an operator, promoter, regulator, and structural genes. The regulator gene codes for a repressor protein that binds to the operator, obstructing the promoter (thus, transcription) of the structural genes. The regulator does not have to be adjacent to other genes in the operon. If the repressor protein is removed, transcription may occur.





Operons are either inducible or repressible according to the control mechanism. Seventy-five different operons controlling 250 structural genes have been identified for E. coli.

Bacteria have flagella, shown in Figure 6, although the bacterial flagellum has a different microtubule structure than the flagella of eukaryotes. Cell walls of bacteria contain the peptidoglycan instead of the cellulose found in cell walls of plants and some algae. Ribosomes are the structures in cells where proteins are assembled. Bacterial ribosomes have different sized ribosomal subunits than do eukaryotes.

Bacteria typically have one of three shapes: rods (bacilli), spheres (cocci) or spiral (spirilla). These shaps are shown in Figures 7 and 8. Unicellular, they often stick together forming clumps or filaments.

Bacterial Reproduction |
Prokaryotes are much simpler in their organization than are eukaryotes. There are a great many more organelles in eukaryotes, as well as more chromosomes to be moved around during cell division. The typical method of prokaryote cell division is binary fission, shown in the animated GIF below as well as in Figure 10. The prokaryotic chromosome is a single DNA molecule that first replicates, then attaches each copy to a different part of the cell membrane. When the cell begins to pull apart, the two chromosomes thus are separated. Following cell splitting (cytokinesis), there are now two cells of identical genetic composition (except for the rare chance of a spontaneous mutation).

Animated GIF of binary fission. Image from: http://www.slic2.wsu.edu:82/hurlbert/micro101/pages/Chap2.html#two_bact_groups



One consequence of this asexual method of reproduction is that all bacterial cells in a colony are genetically the same. When treating a bacterial disease, a drug that kills one bacteria of a specific type will normally kill all other members of that clone (colony) it comes in contact with. Evolution requires genetic variation on which to operate. How then can bacteria increase their genetic variation if their typical mode of reproduction produces clones?

Bacteria can accomplish genetic recombination in three ways. Conjugation, shown in Figures 11 and 12, is the process where one bacterium passes DNA to another through a tube (the sex pilus) that temporarily joins the two conjugating cells. Conjugation occurs only between bacteria in same or closely related species. Transformation involves a bacterium taking up free pieces of DNA secreted by live bacteria or released by dead bacteria. into the surrounding environment. Recall that Griffith's experiment demonstrated this process. The third process, transduction, happens when bacteriophage transfer portions of bacterial DNA from one cell to another.

Certain types of bacteria can "donate" a piece of the their DNA to a recipient cell. The recombination is the bacterial equivalent of sexual reproduction in eukaryotes. Note that the entire DNA is not usually transferred, only a small piece.

Plasmids sometimes carry genes for resistance to antibiotics. Since they are also DNA, plasmids can be transferred between bacteria by any of the three processes mentioned above. Since genetic recombination does not routinely happen (as it does in sexually reproducing eukaryotes), mutation is the most important source of genetic variation for evolutionary change. Normally bacteria have short generation times, mutations are generated and distributed throughout bacterial populations more quickly than in eukaryotes. Prokaryotes have only a single chromosome, which makes them haploid. Consequently, mutations are not hidden by a dominant allele, and will be expressed and evaluated by natural selection more rapidly than in diploid eukaryotes.

Endospores are a method of survival, not one of reproduction. The formation of an endospore is shown in Figure 13. Certain bacteria will form a spore inside their cell membrane (an endospore) that allows them to wait out deteriorating environmental conditions. A small portion of cytoplasm and a chromosome copy are surrounded by three heavy, protective spore coats. The part of the bacterial cell outside the endospore deteriorates and the endospore is released. Endospores allow bacteria that produce them to survive in the harshest of environments. When conditions once again become suitable, the endospore absorbs water and grows out of its spore coat.

Certain disease causing bacteria (such as Bacillus anthracis, the cause of the disease anthrax) can be virulent (capable of causing an infection) for up to 1300 years after forming their endospore! Because of this, as well as other factors, the anthrax bacterium has been considered as a possible biological weapon. Following the September 11, 2001 terrorist attacks, several people died from anthrax exposure, and one postal facility was closed (as was the U.S. Senate building) for several weeks. As of March 2003, no connection between these events has been definitely established.

Classification of Bacteria |
Bacteria are classified on the basis of their method of energy acquisition. Traditional classifications include chemosynthetic, photosynthetic, and heterotrophic groups. Molecular and cladistic studies are reshaping these traditional groups. In the absence of a consensus the traditional groups are employed here..

Chemosynthetic Bacteria
Chemosynthetic bacteria are autotrophic, and obtain energy from the oxidation of inorganic compounds such as ammonia, nitrite (to nitrate), or sulfur (to sulfate).

Photosynthetic Bacteria
Photosynthetic bacteria carry out conversion of sunlight energy into carbohydrate energy. Cyanobacteria, an example of which is shown in Figure 13, are the major group of photosynthetic bacteria. Some early cyanobacteria may have formed the oxygen released into the early atmosphere, transforming our planet from one with an oxygen-free atmosphere, to the modern one that has a significant amount of oxygen present.. In addition to chlorophyll a, cyanobacteria also have the blue pigment phycocyanin and the red pigment phycoerythrin.

Eukaryotic autotrophs all have chloroplasts in which the photosynthetic process occurs. The typical chloroplast organization has thylakoids surrounded by a fluid-like stroma. The chloroplast is a membrane bound organelle. Prokaryotes by definition lack such structures. How can bacteria carry out photosynthesis? The answer is shown in Figure 14. By infolding their cell membrane, prokaryotic autotrophs form thylakoids, in effect turning the bacterium into a single chloroplast.




More primitive photosynthesizing bacteria (e.g., green sulfur bacteria and purple sulfur bacteria) use only photosystem I that contains bacteriochlorophyll. In this style of photosynthesis, no O2 is formed, since hydrogen sulfide (H2S) is used as an electron and H+ donor instead of H2O.

Heterotrophic Bacteria
Members of this large and diverse group must derive their energy from another organism by feeding. Two main types: saprophytic and symbiotic. Saprophytes feed on dead or decaying material and are important nutrient recyclers. Symbiotic bacteria live within a host multicellular organism and contribute to the health of the host. Examples include cows and other grazing animals: the bacteria convert cellulose from plant leaves and stems eaten by the animal into glucose for digestion by the animal. Normally cellulose is nondigestible.

Possible symbiosis of bacteria within early eukaryotic cells was a major step in the evolution of eukaryotic cells. In 1980, Lynn Margulis proposed the theory of endosymbiosis, diagrammed in Figure 15, to explain the origin of mitochondria and chloroplasts from permanent resident prokaryotes. According to this idea, a larger prokaryote (or perhaps early eukaryote) engulfed or surrounded a smaller prokaryote some 1.5 billion to 700 million years ago.

Instead of digesting the smaller organisms the large one and the smaller one entered into a type of symbiosis known as mutualism, where both organisms benefit and neither is harmed. The larger organism gained excess ATP provided by the "protomitochondrion" and excess sugar provided by the "protochloroplast", while providing a stable environment and the raw materials the endosymbionts required. This is so strong that now eukaryotic cells cannot survive without mitochondria (likewise photosynthetic eukaryotes cannot survive without chloroplasts), and the endosymbionts cannot survive outside their hosts. Nearly all eukaryotes have mitochondria. Mitochondrial division is remarkably similar to the prokaryotic methods that will be studied later in this course. A summary of the theory is available by clicking here.

A vital symbiosis that bacteria seem to have participated in for hundreds of millions of years is their relationship with plants, both as soil nitrogen-fixing bacteria, as well as internal guests in the root nodules of plants of the pea family. Most organisms cannot use atmospheric nitrogen (N2) directly. Some bacteria have the metabolic pathways to convert inorganic N2 into various forms of organic nitrogen. Mutualistic nitrogen-fixing bacteria, such as Rhizobium, live in nodules on the roots of soybean, clover, and alfalfa plants (all members of the pea family, Fabaceae), where they reduce N2 to ammonia (NH4) to the benefit of both themselves as well as their their host. These bacteria also benefit by using some of a plant's photosynthetically produced organic molecules.

Plants need nitrogen for many important biological molecules including nucleotides and proteins. However, the nitrogen in the atmosphere is not in a form that plants can utilize. Many plants have a symbiotic relationship with bacteria growing in their roots: organic nitrogen as rent for space to live, as shown in Figure 16. These plants tend to have root nodules in which the nitrogen-fixing bacteria live.

All the nitrogen in living systems was at one time processed by these types of bacteria, which took atmospheric nitrogen (N2) and modified it to a form that living things could utilize (such as NO3 or NO4; or even as ammonia, NH3 in the example shown below in Figure 17).



Not all bacteria utilize the above route of nitrogen fixation. Many that live free in the soil, utilize other chemical pathways, as shown in Figure 18.

Many heterotrophic bacteria also cause diseases such as strep throat, rheumatic fever, cholera, gonorrhea, syphilis, and toxic shock syndrome. Bacteria can cause disease by destroying cells, releasing toxins, contaminating food, or by the reaction of the body to the infecting bacteria. Bacterial infections can be controlled by vaccinations and antibiotic treatments. Antibiotics interfere with some aspect of the replication of bacteria, and are produced by microorganisms such as fungi, that compete with bacteria for resources. Penicillin, the first antibiotic discovered, inhibits the synthesis of new cell walls in certain types of bacteria. However, the overuse of antibiotics during the past fifty years has led to natural selection favoring antibiotic resistance. There are reportedly more than 50 strains of antibiotic resistant bacteria, necessitating the development of new antibiotics and the frequent change of antibiotics in treatment.

Peptic ulcers result when these protective mechanisms fail. Bleeding ulcers result when tissue damage is so severe that bleeding occurs into the stomach. Perforated ulcers are life-threatening situations where a hole has formed in the stomach wall. At least 90% of all peptic ulcers are caused by Helicobacter pylori. Other factors, including stress and aspirin, can also produce ulcers.

Gonorrhea and syphilis are among the most common bacterially caused sexually transmitted diseases. Both can be treated and cured with antibiotics, once diagnosed. Once considered likely to result in death, syphilis is usually curable with antibiotics, although overuse of antibiotics can reduce their effectiveness.

Treponema pallidum is the bacterial species that causes syphilis. Syphilis is transmitted from an infected person to an uninfected one by direct contact with a syphilis sore during vaginal, anal, or oral sex. Proper use of condoms has been shown to reduce the incidence of syphilis. Syphilis sores occur mainly on the genitals, vagina, anus, or in the rectum, as well as on the lips and inside the mouth. Infected, pregnant women can pass it to their unborn child. The urban myth about getting this disease from a toilet seat is untrue. Syphilis cannot be spread by toilet seats, door knobs, swimming pools, hot tubs, bath tubs, or sharing of clothing or eating utensils. There are three stages to the disease. The prim,ary stage is the time between infection and the start of the first symptom, ranging from 10-90 days. The primary stage normally in indicated by the appearance of a single sore also known as a chancre. The chancre is usually round, firm, small and painless, and appears where syphilis entered the body. If proper treatment is not utilized, the diease moves into the secondary stage. The second stage occurs when some area(s) of the skin develop an itchless rash. Rashes can appear as the chancre is fading or can be delayed for weeks. The rash often appears as rough, red or reddish brown spots both on the palms of the hands and on the bottoms of the feet. The rash also may also appear on other parts of the body.. Even without treatment, rashes clear up on their own. In addition to rashes, second-stage symptoms can include fever, swollen lymph glands, sore throat, patchy hair loss, headaches, weight loss, muscle aches, and tiredness. The disease can pass to sex partners when primary or secondary stage symptoms are showing. The latent, or hidden, stage of syphilis initiates when the symptoms of the second stage disappear. Without treatment, an infected individual still has syphilis, even though he or she does not display symptoms. Treponema pallidum remains in the body, and so may begin to damage internal organs, suc as the brain, nerves, eyes, heart, blood vessels, liver, bones, and joints. This internal damage may not show up until many years later when the person enters the late or tertiary stage of syphilis. Late stage symptoms include the inability to coordinate muscle movements, paralysis, numbness, gradual blindness and dementia. This damage may be serious enough to cause death. Because of this progress of ther disease, often resulting in death, the disease was one greatly feared before the advent of antibiotics.

Gonorrhea is another common sexually transmitted disease caused by Neisseria gonorrhoeae, a bacterium. This bacterium can grow in the reproductive tract, including the cervix, uterus, and fallopian tubes in women, as well as in the urethra in both men and women. The bacteria can also grow in the mouth, throat, and anus. Gonorrhea is spread through vaginal, oral, or anal sexual contact. Ejaculation does not have to occur for gonorrhea to be transmitted or acquired. Gonorrhea can also be transmitted during birth. Symptoms include a burning sensation during urination and a yellowish white discharge from the penis. Some infected males may have painful or swollen testicles. Many women often do not show strong signs of the early symptoms of gonorrhea. The initial symptoms for women include a painful or burning sensation upon urination, as well as a yellow or occasionally bloody vaginal discharg. Women with no or mild gonorrhea symptoms are still at risk of developing serious complications from the infection. Untreated gonorrhea in women can develop into pelvic inflammatory disease. Rectal infection has symptoms such as discharge, anal itching, soreness, bleeding, and sometimes painful bowel movements. Infections in the throat cause few symptoms. Penicillin is a common antibiotic no longer used to treat gonorrhea due to the development of penicillin-resistant strains of the gonorrhea bacterium.

Salmonella is a genus of rod-shaped bacterium whose species cause typoind fever and similar illnesses. The bacteria of this genus are widespread in animals, especially in poultry and pigs. Environmental sources of the organism include water, soil, insects, kitchen surfaces, feces, and raw meat, seafood, and poultry.



The Archea |
The most primitive group, the archaebacteria, are today restricted to marginal habitats such as hot springs or areas of low oxygen concentration. Archaebacteria (now more commonly referred to as the Archaea) are considered among the oldest and most primitive types of organisms known. They have significant differences in their cell walls and biochemistry when compared to the bacteria. These differences are sufficient in most schemes, to place the Archaea into a separate kingdom or domain. Under the three domain model, they are the taxonomic equivalents of the other bacteria and the eukaryotes. It is thought that since bacteria and Archaea inhabit some of the modern environments thought by paleontologists to resemble what the early Earth was like, that both are descended from a common ancestor. The Eukarya later split from the Archaea.

The archeans are life's extremists, occupying environments that "normal" organisms find too harsh. Three types of archaebacteria: methanogens, halophiles, and thermacidophiles. They live in extreme habitats.

The methanogens are chemosynthetic archeans that produce methane (CH4) from hydrogen gas and CO2. Both ATP synthesis and CO2 reduction are linked to this reaction. Methanogens can decompose animal wastes to produce methane, which can be collected and combusted to make ecological friendly electricity. Pollutants from methane combustion are much fewer than from combustion of coal.

There are three groups of Archaea. The methanogens live under anaerobic environments (e.g., marshes) where they produce methane. Halophiles require high salt concentrations (such as in Utah's Great Salt Lake). Thermoacidophiles live under hot, acidic environments (like those found in geysers).

The Fossil Record |
Fossil evidence supports the origins of life on earth earlier than 3.5 billion years ago. Specimens from the North Pole region of Western Australia are of such diversity and apparent complexity that even more primitive cells must have existed earlier. Rocks of the Ishua Super Group in Greenland yield possibly the fossil remains of the earliest cells, 3.8 billion years old. The oldest known rocks on earth are 3.96 Ga and are from Arctic Canada. Thus, life appears to have begun soon after the cooling of the earth and formation of the atmosphere and oceans.

These ancient fossils occur in marine rocks, such as limestones and sandstones, that formed in ancient oceans. The organisms living today that are most similar to ancient life forms are the archaebacteria (the archaea in modern usage). This group is today restricted to marginal environments. Recent discoveries of bacteria at mid-ocean ridges add yet another possible origin for life: at these mid-ocean ridges where heat and molten rock rise to the earth's surface.

Many of the ancient phototrophs and heterotrophic bacteria lived in colonial associations known as stromatolites. Cyanobacteria are on the outer surface, with other photosynjthetic bacteria (anoxic) below them. Below these phottrophs are layers of heterotrophic bacteria. The layers in the stromatolites are alternating biogenic and sedimentologic in origin. A modern day stromatolite is shown in Figure




Learning Objectives |
Review the characteristics of life from the first chapter. Which of these is/are present in bacteria? Which is/are absent?
How does parokaryotic cell structure differ from that of the eukaryotes?
How do prokaryotic and eukaryotic cell division processes differ? What must occur in any type of cell division?
List the significance, to humans, ecology, and other things, of bacteria.
Be able to list the main steps in the nitrogen fixing process commonly used by bacteria.
Be able to explain to a fellow student how mycorrhizae fungi actually help a plant when they infect it.
Use the Internet to locate information about a bacterially caused human disease. What treatments are available?
Review Questions |
Which of these is not a typical shape for a bacterial cell? a) rod; b) spiral; c) spherical; d) all are typical bacterial shapes. ANS is d
Bacteria divide to produce new cells using which of the following processes? a) mitosis; b) binary fission; c) meiosis; d) karyogamy ANS is b
Bacteria have which of these structures in common with eukaryotes? a) nucleus; b) miotchondria; c) ribosomes; d) endoplasmic reticulum ANS is c
The oldest known fossils on Earth are most similar to ___. a) animals; b) plants; c) fungi' d) bacteria ANS is d
Bacteria are important as ___. a) food; b) decomposers; c) producers of antibiotics and other medicines; d) all of these ANS is d
The form of nitrogen listed below that can be utilized by most living things is ___. a) N2; b) H2NO3; c) NH4; d) none of these can be used in their listed form by living things. ANS is c.
If two organisms are in a symbiotic relationship and one causes harm to the other, that relationship is described as ___. a) parasitism; b) communism; c) mutualism; d) capitalism ANS is a
Photosynthesis by bacteria produced ____ as a waste product. a) glucose; b) carbon dioxide; c) oxygen; d) all of these are produced by photosynthesis. ANS is c
Thylakoids are ___. a) infoldings of the bacterial plasma membrane on which the enzymes of aerobic respiration are located; b) not found in photosynthetic bacteria; c) infoldings of the bacterial plasma membrane on which the enzymes of photosynthesis are located; d) structures only found in eukaryotic chloroplasts. ANS is c
Which of these is a bacterially caused disease? a) herpes; b) syphilis; c) AIDS; d) Huntingdon's Disease. ANS is b
Which of these bacterial diseases is spread by sexual contact? a) gonorrhea; b) salmonella; b) typhoid fever; d) food spoilage ANS is a
Links |
Cells Alive! Very interesting site with new features each month. Of note here are sections dealing with bacteria and diseases.
The Nanoworld Image Gallery Lots of interesting pics and links for microscopes.
Stromatolites: Earth's Earliest Life Forms from Western Australia This Geological Survey of Western Australia site gives excellent illustrations and clear information about the stromatolites from Western Australia that are among the oldest known fossils.
Major Groups of Prokaryotes Images and text illustrating the types and significance of major groups of prokaryotic cells. Site by Kenneth Todar University of Wisconsin-Madison Department of Bacteriology/
The Microbe Zoo What are they? Where are they? Why should I care? Answer these questions at this site.
The Five Kingdoms A table summarizing the kingdoms of living things.
The Bad Bug Book US FDA information on bacterially caused diseases.
Fundamentals of Microbiology 101 This Washington State University page is aimed at non-biology majors...a great resource for microbiology for the general student population.
Bacteria: Life History and Ecology UCMP Berkeley
Introduction to the Bacteria UCMP Berkeley
Introduction to the Cyanobacteria UCMP Berkeley
Cyanobacteria Morphology and Introduction to the Archaea Life's extremists. . . These University of California Berkeley sites offer some pertinent information about a group of living organisms that resemble some of the earliest known fossils.
Life on Mars? American Association for the Advancement of Science (AAAS) Symposium on a monumental discovery...or was it? "Surrender earthling!"
References |
Schopf, J. W. 1999 Cradle of Life: The Discovery of earth's Earliest Fossils. Princeton University Press, 367 p.


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