In the context of this course, micro-organisms are often a causative agent in a large number of infectious diseases whose presence can be easily traced throughout recorded history. Early victims of microbial infections and epidemics may not have understood the microbiology behind the disease, but they certainly understood the consequences of the epidemics in their communities. This section will briefly introduce a few core microbiological concepts.

Microbiology is the study of microscopic organisms which include many life-forms:

	Bacteria - simple, single cell
	Fungi - single & multi cell forms - yeast,  filamentous molds,  complex fungi
	Protists - single cells, some multicellular  -  algae,  protozoans,  slime molds
	Viruses - acellular,  protein-based lifeforms, typically intracellular parasites

Microbiology is not a new field of study. In 1674 Anton van Leeuwenhoek  used simple, self-made  microscopes to examine stagnant H₂O, where he observed "wee animalcules"  - microscopic organisms. 

His detailed descriptions and drawings of these microscopic forms of life were published by the  Royal Society of London. Many others also made significant contributions including Louis Pasteur, Edward Jenner and Robert Koch as a few examples.

Areas of Microbiology

Microbiology can be examined in a number of ways, although focusing on the nature of specific micro-organisms or on health-related aspects are the most common.

Organization by Organisms

1. Bacteriology – study of bacteria

2. Virology  - study of viruses

3. Parasitology – study of parasites

4. Mycology – study of fungi

5. Phycology - study of algae

6. Protozoology – study of protozoa

Organization by Health Science

1. Epidemiology – study of disease patterns in populations

2. Etiology – identification of agents which cause disease

3. Immunology – study of immunological responses to micro-organisms

4. Infection control – control of spread of infectious disease

Areas of Study and Research

In addition to being causative agents of infectious diseases there are many other aspects of microbiology which need to be understood. As normal flora in humans (or other living systems) there are significant benefits with respect to metabolic functions as well as preventing invasion by pathogens (positive antagonistic effects). In the environment micro-organisms serve many beneficial roles in the food chain, as decomposers, in sewer / wastewater treatment, etc. In industry micro-organisms are essential components of the food production, brewing / beer production, pharmaceutical industries and many other areas.

Micro-organisms survive in every possible environment, including those that are considerable inhospitable. The air we breathe, the water, soil, our skin surface, our intestines - all harbor thousands of microscopic organisms.

There are a number of ways of classifying micro-organisms, including division into the Kingdom Protista (bacteria) and Eukaryotes (animal-type cells). The main differences are described below.

 

The (2) Fundamental Cell Types

1. Eukaryotic  (“true nucleus”)  -  more complex

2. Prokaryotic  (“pre-nucleus”)  -  simpler, smaller

Eukaryotic Cells

            1.  Nucleus - eukaryotes have a "true nucleus”.

	Genetic / nuclear material surrounded by a nuclear membrane.
	Genetic / nuclear material organized into paired chromosomes.
	Nuclear membrane (DNA) associated with proteins called histones.
	Nucleus contains nucleolus - sites of ribosome synthesis.

            2.  Complexity - internal structure more complex - has "organelles"

            3.  Cell walls

	Found only in plant cells, fungi
	Composed of cellulose, chitin.

            4.  Replication / division occurs by mitosis, meiosis.

 

Prokaryotic Cells

            1.   Nucleus - no “true” nucleus.

	lack a nuclear membrane.
	lack histones.
	lack nucleolus.

            2.   Complexity - No organelles.

     3.   Cell walls

	All typical prokaryotic cells possess cell walls.
	Cell walls made of a peptidoglycan layer.

4.   Replication / division - binary fission.

       Examples Micro-organisms of each cell type :

            1.  Eukaryotes - fungi, protozoa, algae

            2.  Prokaryotic - bacteria

            3.  Viruses - belongs in neither group - (acellular, protein-RNA based lifeforms) 

 Growth of Micro-organisms

1.    Reproduction - Generation Times

	Doubling time - time required for one cell to produce two new cells.
	Varies with type, age and health of  organism and environmental conditions.
	Can range from 15 min. to as much as 24 hrs.)
	Population constantly doubles - increases exponentially

2.   Measuring Bacterial Growth

	Plate count (standard plate counts)
	Direct microscopic count
	Turbidity / optical density

3.  Phases of Growth

Micro-organisms move through four stages of growth including lag, logarithmic, stationary and death phases:

http://www.dentistry.leeds.ac.uk/OROFACE/PAGES/micro/expgrow.gif

Lag Phase:

	increased metabolic activity
	no increased  number of cells
	cells are preparing for reproduction and accumulating nutrients and energy

Exponential / Logarithmic Growth Phase (Log Phase)

microbial population is constantly doubling - rapid growth / reproduction

diagnostic testing and  antibiotic therapies most effective in this phase

Stationary Phase

	population numbers are static: rate of reproduction = rate of death
	occurs due to exhaustion of nutrients, accumulation of wastes, etc..

Death Phase

	rate of death higher than rate of reproduction.
	rate of death is species-variable

 

Parameters Influencing Bacterial Growth

Microbial populations are both extraordinarily adaptable and yet can be remarkably sensitive to "rate limiting" environmental conditions. Example factors which may influence growth can include:

1. Temperature -  all bacteria  have an optimum temperature range. Based on temperature sensitivity there are three categories of micro-organism:  Mesophiles (20°C - 50°C),  Thermophiles (50° - 80°C)  Hyperthermophiles) - up to 110°C and Psychrophiles  (0°C  - 20°C)

2. Nutrients - fundamental nutritional requirements include Carbon,  Nitrogen, Hydrogen, Oxygen as well as trace elements and minerals.  As well, there may be a requirement for special growth factors for more fastidious organisms. These requirements could include vitamins, amino acids, carbohydrates, blood factors

3. Classification by Nutrient Source

   	Autotrophic - independent - require light, inorganic compounds
   	Heteroptrophic - dependant  - require organic compounds

4. Oxygen and other Gases - there are four groups of micro-organisms based on oxygen needs:

   	Aerobic - require gaseous molecular oxygen
   	Anaerobic - do not require gaseous oxygen, acquire chemically
   	Facultative - aerobes or anaerobes as environment dictates

5. Moisture - each organism has a minimum requirement for water. In addition to forming the cytosol, water levels affect osmotic pressure (the pressure exerted by concentration of solutes in water).  This osmotic pressure can have a profound impact on most organisms.

6. pH -  most micro-organisms have a range of pH values over which they function well. With acidic or basic conditions outside of this range there can be a significant drop in survival as enzymatic systems and metabolism shuts down. Acidophiles prefer a range of pH 0-5, Neutrophiles  ~ 7.0, and Alkalinophiles pH 8-12.

7. Salinity - closely related to moisture requirements and osmotic pressure. Some micro-organisms can survive much higher levels of salt. Halophillic organisms require 3% salt but may range as high as 15-30% salt levels.

Nomenclature and Microbial Taxonomy

One of the most cited taxonomic references for microbial classification is  Bergey’s Manual (of Systematic Bacteriology) which describes physiological characteristics and chemical testing.   In general, the prokaryotes are classified using the following taxonomic groups:

Division -- Class -- Order -- Family -- Genera -- Species -- Strain

 

Techniques used to Classify Bacteria

Bacteria represent a significant source of pathogenic infections in humans. There are many ways to classify bacteria. Examples include:

	cell morphology - size and shape (rods, spheres, spiral)
	colony shape (on petri plates)
	stain uptake (use of characterizing stains- i.e. Gram stains)
	motility (mobile / immobile)
	energy sources (autotrophs, heterotroph, etc.)
	growth requirements (pH, salinity , oxygen, nitrogen)
	products (fermentation / growth products)
	antibiotic response and sensitivities
	Cell wall composition.
	Nucleic acid  profiling (sequence comparisons)
	Serotyping and immunological testing
	RFLP analysis and genetic hybridization

 

Examples of Bacterial Morphology
The following table describes the core classification of bacteria by groups:

Section:	Example of Genus:	Habitat:
Spirochaetes	Treponema	Parasites of animals
Microaerophilic Gram-negative curved rods	Spirillum	Aquatic, animal parasites
Aerobic Gram-negative rods	Pseudomonas	Soil, water, animal parasites
Facultatively Anaerobic Gram-negative rods	Salmonella	Intestinal tracts, animal parasites
Anaerobic Gram-negative rods	Bacteroides	Animal, insect parasites
Sulphate reducers	Desulfovibrio	Anoxic sediments
Anaerobic Gram-negative cocci	Veillonella	Animal intestines
Rickettsias, Chlamydias	Rickettsia	Arthropods, animal parasites (obligate intracellular)
Mycoplasma	Mycoplasma	Animal, plant parasites, no cell wall
Endosymbionts	Holospora	Symbionts of protozoans, insects, plants
Gram-positive cocci	Staphylococcus	Animal pathogens
Endospore formers	Bacillus	Soil, animal pathogens
Regular Gram-positive rods	Lactobacillus	Dairy products, animal intestines
Irregular Gram-positive rods	Corynebacterium	Soil, animal pathogens
Mycobacteria	Mycobacterium	Soil, plants, animal pathogens
Nocardioforms	Nocardia	Soil
Appendaged bacteria	Caulobacter	Aquatic, soil
Sheathed bacteria	Sphaerotilus	Aquatic
Sliding bacteria	Cytophage	Aquatic
Fruiting bacteria	Myxococcus	Soil
Aerobic lithotrophs	Nitrobacter	Soil, water
Archaeobacteria (archaea)	Halobacterium	Extreme environments
Anoxygenic phototrophs	Chromatium	Waters
Oxygenic phototrophs	Anabaena	Soil, water
Actinomycetes	Streptomyces	Soil

http://www-micro.msb.le.ac.uk/109/Systematics.html

Enumeration of Cells

Numbers of microorganisms can be estimated based using a number of techniques which include conducting representative cell counts (on plates or other media).  Direct microscopic counts are conducted by examining a known volume of cell suspension under a microscope. Direct microscopic counts enumerate living and dead cells equally. The use of stains (i.e. Gram stain, etc.) can increase visibility and allow for both qualitative and quantitative assessments.