Bacteriology at UW-Madison

The Microbial World

Lectures in Microbiology by Kenneth Todar PhD    University of Wisconsin-Madison    Department of Bacteriology

Introduction to The Microbial World

Figure 1. The bacterium, Legionella. American Society for Microbiology.

The Microbial World

The microbial world is a realm of life made up of microorganisms and viruses. Microbiology is the branch of biological sciences concerned with the study of these microbes.

Microorganisms are unicellular organisms (capable of existence as single cells), too small to be seen with the naked eye. Among all forms of life on the earth, microorganisms predominate in numbers of species and in biomass, but their occurrence is generally underappreciated because of their small size and the need for a microscope to see individual cells. Although a light microscope is generally required to visualize a single microbial cell, microbial colonies and communities can readily be observed in nature. As discussed below, viruses are noncellular entities and cannot be considered microorganisms. Viruses and cellular microorganisms are considered microbes.

Figure 4. The cyanobacterium Anabaena. American Society for Microbiology. Two (not uncommon) exceptions that microorganisms are unicellular and undifferentiated are seen in Anabaena. The organism lives as a multicellular filament or chain of cells. The predominant photosynthetic (bright yellow-green) cells conduct photosynthesis, while the obviously large "empty" cells occasionally seen along a filament are differentiated cells in which nitrogen fixation, but not photosynthesis, takes place.

Cell Theory

To understand microbes it is necessary at the outset to review the basic concepts of biology regarding cells. A cell is considered to be the fundamental unit of life and an understanding of cell theory is the basis for the understanding of life, including microbial life. The main points of the cell theory are as follows:

1. All organisms are composed of basic membrane-enclosed units called cells.
2. All organisms are either unicellular (single cells) or multicellular (more than one cell).
3. All cells are fundamentally alike with regard to certain aspects of their chemistry, structure and metabolism.
4. Cells arise from previously existing cells by means of asexual or sexual reproduction.
5. Cells can mutate and evolve into new or different types of cells.

Basically, a cell is a membrane-enclosed entity capable of self replication, mutation, and maintenance of genetic continuity.

Figure 5. A model cell, the fundamental unit of life, in this case a procaryotic cell. A cell consists of a membrane that encloses the cell cytoplasm. The cytoplasm contains a nuclear region (DNA), which functions as the genetic center; ribosomes, which are required for the synthesis of proteins; enzymes and chemical precursors of cell material that are in solution in water. The membrane and enzymes carry out the functions of life as directed by the DNA. Most, but not all microbes have a cell wall, also present in plant cells but notably missing in animal cells.

Properties of living systems

 Bios means life, and biology is the study of life, but biologists have a difficult time defining life. It is easier to describe life than it is to define it. Life can be described as a system having the following properties. By one strategy or another, all living organisms exhibit the se characteristics.

1. Cellular organization
2. Ability to produce energy and to transform chemicals into cell material
3. Ability to reproduce, and in doing so, pass their genes (DNA) to their progeny
4. Ability to respond to external and internal stimuli
5. Ability to grow, and in the case of some unicellular and all muticellular organisms, to develop or differentiate into various types of cells

The term organism is a descriptive term that implies cellular life.  Hence, micro-organisms are a type of cellular life that is microscopic in size.  Viruses are not considered microorganisms because they are not cells. Viruses consist of nucleic acid (DNA or RNA) enclosed in a protein coat They lack many essential properties of cells, including membranes, ribosomes and metabolic enzymes. Viruses are considered microbes, but not microorganisms, and arguably are not "alive".

Procaryotic and Eucaryotic Cells

Biologists recognize the existence of two fundamentally different types of cells in the microbial world, called procaryotic and eucaryotic cells.  (Greek, pro, before + cary, kernel or nucleus + eu, true). Eucaryotic cells have a "true" nucleus (the region of the cell that contains genetic information or DNA) because it is enclosed in a nuclear membrane;  procaryotic cells are said to have a "primitive" nucleus because their DNA is not enclosed within a nuclear membrane. The nuclear region of a procaryotic cell is sometimes referred to as a nucleoid, but never as a nucleus.

Figure 6. Drawing and electron micrograph of a typical procaryotic cell (top) and a typical eucaryotic cell (bottom). The definitive characteristic of a eucaryotic cell is the presence of a nuclear membrane that encloses the nuclear material. Bacteria and archaea are procaryotic; algae, fungi and protozoa, as well as plants and animals, are eucaryotic.

There are five major groups of microorganisms, Archaea, Bacteria, Algae, Protozoa, and Fungi. Archaea and Bacteria are procaryotic cells. Unicellular algae and protozoa (collectively referred to as protista) and fungi are eucaryotic cells, similar to plants and animals.  This is one of the most important and significant lines of demarcation within the microorganisms and should be appreciated before an introduction to the various groups of microbes. 

Kinds of Microbes

Archaea are a group of unicellular procaryotic cells that sometimes produce methane (CH₄) during their metabolism, and which often live in extreme environments such as high temperature, low pH or high salt concentrations. They are specifically adapted to these conditions by means of special types of membranes and metabolism.

Figure 7. A hydrothermal vent on the floor of the Pacific Ocean injects superheated steam and hydrogen sulfide (H₂S) into the environment. Archaea that use the H₂S for energy are found near such thermal vents growing at temperatures as high as 120^oC.

Bacteria are also unicellular procaryotic organisms. They have a unique type of cell wall and cell membrane that distinguishes them from Archaea. Bacteria live everywhere that life exists on earth except the most extreme environments, including in associations with animals and plants. Most are beneficial or harmless, but some cause disease.

Figure 8. (L) Clostridium botulinum, the bacterium that causes botulism is also the source of BOTOX. (R) Salmonella enterica the most common cause of salmonella food poisoning.

Algae are plant-like, photosynthetic, eucaryotic organisms that live wherever there is light and moisture. They convert carbon dioxide (CO₂) to organic material and produce oxygen (O₂) during photosynthesis, the same as plants.

Figure 9. Monadus subterraneous, a freshwater alga.

Protozoa are animal-like, nonphotosynthetic eucaryotes common in moist environments, including the intestinal tracts of animals. Most protozans are motile because they are predatory on other microbes and have to catch and ingest their food. A few of them cause some important diseases, such as malaria and sleeping sickness.

Figure 10. The protozoan, Paramecium.

Fungi are nonphotosynthetic eucaryotes, generally non-motile, that absorb their nutrients directly from the environment. The kingdom includes mushrooms, molds and yeast. Yeast are truly unicellular, while molds and mushrooms, although they have a vegetative multicellular stage, produce unicellular spores. Molds live mainly in the soil and are responsible for the decomposition (biodegradation) of organic material. They are also an important cause of plant disease and food spoilage. Molds grow by filament formation and form reproductive structures (spores) that are spread by wind and water. Yeast reproduce by budding and live in environments high in sugar. They metabolize sugars to produce ethanol and carbon dioxide. A couple are pathogens of humans.

Figure 11. A fruiting body of the common mold, Aspergillus nidulans, which contains the microscopic spores of the fungus.

Viruses are made up of nucleic acid (DNA or RNA) and protein and have some of the characteristics of life. But they lack ribosomes (for protein synthesis), membranes, and  means to generate energy, which are properties of cells. The study of viruses developed within the field of bacteriology, and virology has developed into a major branch of microbiology. Viruses should considered microbes, but they are not microorganisms since they are noncellular.

Viruses are considered obligate intracellular parasites because they can only replicate in association with a host cell which they infect. All kinds of cells -- plant, animal and microbial -- are susceptible to virus infections. Since cell damage results from most viral infections, viruses are agents of disease. Although viruses are too small to be seen by conventional light microscopy, they can be visualized and photographed by means of electron microscopy.

Figure 12. The West Nile Virus. electron micrograph.

Microbial Habitats

Microorganisms live in widely diverse habitats ranging from boiling hot springs to the Antarctic ice shelves; in all types of terrestrial environments and in the farthest depths of the ocean; and in intimate associations with all other forms of life, including plants, insects, animals and humans. In all natural habitats that support life on earth, microbes will be found to flourish. Anywhere where higher (visible) forms of organisms  exist, microbes will always be present. The general answer to where microbes will be found is in all natural environments where liquid water occurs.

Figure 14. Some bacteria that live on the surfaces of the human body. Gram stains. 1000X mag. 1. Staphylococcus epidermidis - skin; 2. Haemophilus influenzae - upper respiratory tract; 3. Bacteroides fragilis - colon; 4. Bifidobacterium bifidus - small intestine; 5. Actinomyces israelii - oral cavity; 6. Lactobacillus acidophilus - vagina.

Branches of Microbiology

Microbiology is both an applied and a basic science. It is not a single subject. It has many areas of specialization including bacteriology, mycology (study of fungi), virology, medical microbiology and immunology, public health, food microbiology, biotechnology, microbial genetics, and cell and molecular biology.

Medical Microbiology and Public Health Microbiology
Medical microbiology is involved in finding ways of identifying, preventing and treating bacterial diseases such as tuberculosis and meningitis, and viral diseases ranging from flu to AIDS. Some fungi cause minor infections such as thrush and athlete's foot, and some can cause more serious infections in people with compromised immune systems. Protozoans cause diseases such as malaria and sleeping sickness that have plagued humanity throughout its existence.

Microbiologists in hospital laboratories deal with samples from patients, isolating and identifying the microbes that cause illness, and giving advice on appropriate  treatment. They also try to prevent patients from acquiring hospital-acquired (nosocomial) infections and they attempt to trace and eliminate any infections which may occur.

Like hospital microbiologists, public health microbiologists isolate and identify pathogens. Their records of cases and outbreaks of microbial infections are analyzed to provide a continuous picture of the progress of infections,  and the information is used by health officials in the control of disease. If there is risk of an epidemic, they suggest preventive measures, such as quarantine or mass immunization programs.

Public health microbiologists also track down the restaurant, kitchen or factory-prepared food that may be the source  of a food poisoning outbreaks, or find the air-conditioning system harboring bacteria responsible for an outbreak of pneumonia. Food, milk and water supplies must also be routinely tested to ensure that they are of good microbiological quality and not contaminated.

Medical microbiology is helping to pioneer gene therapy techniques against genetic disorders such as cystic fibrosis and inherited cancers. For example, viruses are used to introduce genes carrying the desired characteristic into the cell nuclei of the host organism. Gene technology also has many applications in the development of medicines and diagnostics.

Medical microbiologists that work in research institutes and universities study topics such as how diseases develop, or the interactions between pathogenic microbes and host cells. Pharmaceutical companies and other industrial research and development agencies may employ medical microbiologists to work on the development of medicines and vaccines.

Food Microbiology
Food Microbiology is concerned with microbial production of foods and with food safety.

Microbial fermentations have been used for centuries to produce foods such as cheese and yogurt and alcoholic beverages like wine and beer. Olives, dill pickles, vinegar and some processed meats are also made by fermentation. The best known fermented products are beer, wine and spirits. Microbiologists are involved at all stages of modern food and drink manufacturing processes. They are involved in the maintenance of the microbial culture (the inoculum) that is used to start the fermentation of the milk or grape juice, to prevent deterioration of  existing strains and to develop or improve existing ones. Some beers are still produced by traditional methods, but in the main, brewing is a strictly controlled operation. Microbiologists maintain the strains of yeasts used and produce improved strains, as well as supervising the fermentation. They also have to solve the problem of dealing with waste materials produced by the process.

Some foods contain other, less obvious, microbial products, such as flavors and colors. Many  factory-produced foods lose important vitamins during processing, and to keep our diet healthy, vitamins are added back to the food (e.g. breakfast cereals). These vitamins are made by high-yielding bacterial strains and are a relatively inexpensive ingredient.

Safety and hygiene are also the concern of microbiologists in the foods industry. As we store food for longer periods, it becomes more difficult to prevent spoilage by microbes. Some spoilage just makes food look unattractive, but food poisoning may be caused by microbial pathogens such as E. coli, Salmonella or Staphylococcus growing on food. The increased demand for production and storage of pre-prepared meals has caused a rise in the number of cases of food poisoning by other bacteria such as Listeria and Campylobacter. Microbiologists are employed in quality control to ensure that products are safe and wholesome, in product development, and in basic research into food hygiene and preservation.

Food microbiologists test the safety of foods

Water Microbiology
Good quality water is needed for domestic and industrial purposes. Rivers and reservoirs supply water to purification plants where microbiological and chemical tests are carried out to check its quality before distribution. The action of bacteria and protozoa in sewage treatment plants breaks down waste material so that effluent can safely be released back into the rivers. Microbiologists in domestic and industrial water companies, in public health facilities, and the EPA monitor and control these processes to ensure the quality and safety of domestic water supplies.

Agricultural Microbiology
Some microbiologists are at work in various aspects of agriculture. Microbes play an important part in agriculture. They fix nitrogen in the soil into a form that can be used by plants as a fertilizer and turn grass into the winter animal feed in the form of silage. Microbiological research in these and other agricultural topics is carried out in universities, institutes and industry.

Farm animals and crops are susceptible to pests and microbial diseases. Veterinary microbiologists and plant pathologists do research and give advice on problems farmers may encounter.

Microbes are also used for biocontrol. Pests or weeds can be sprayed with a microbe that attacks them instead of spraying crops with pesticides or herbicides which kill many types of harmless organisms. Biocontrol has great potential, particularly in developing countries where a sustainable method of crop protection is the preferred approach.

Environmental Microbiology
Microbiologists in research institutes and universities study the ecology of microbes in soil, fresh water, the sea, and other habitats. Microbial activities can be harnessed to avoid or minimize environmental pollution. Factory wastes are treated with suitable cultures or enzymes produced from bacteria. Microbes can also be used in production processes. For example, microbes can be used to replace harmful chemicals in dye production and leather processing.

Some parts of our environment are already badly damaged by pollution. Industrial processes (and accidents) have left land and water contaminated with such things as petroleum products, toxic heavy metals, phenolic compounds, pesticides and insecticides. Microbial processes are being developed to clean up such pollution - a process known as bioremediation.

Microbiology as a Basic Science

Basic research
About half the work force of microbiologists is involved in basic research with microorganisms. These microbiologists are housed in university, government and institutional laboratories, wherein they utilize microorganisms to study and learn about their fundamental biological characteristics that stem from their structure in relationship to function, their physiology or metabolism, and their genetics and genetic systems. Because of the unification of all forms of life that contain the same type of genetic material and have similar types of metabolism, what is learned about these processes in simple unicellular organisms is applicable to all types of living organisms, including so called "higher organisms" i.e., plants and animals.

Because of the ease of manipulation of microbes in the laboratory, as well as their rapid generation times (as little as 15 minutes) compared to many months or years for animals, many of the principles of molecular and cell biology and genetics are more readily studied in a microbe than in a rat or a human. Thus, the bacterium Escherichia coli (E. coli) has had more scientific papers written about it than any other organism except Homo sapiens.

Basic research is, of course, not without value to society. Many of the discoveries, made intentionally or by accidental observation in basic research with microbes,  have resulted in huge advances in medicine and agriculture and food science.