What is Microbiology?


Have you ever wondered about how small germs are?
And what are germs anyway?
Are you always being told to wash your hands?  Do you know why?

The tiny things you know of as germs are known as bacteria by scientists.  They are very small and you can't see them.   Many thousands could fit on a pin head.  They are alive, in the same way that you are, or a dog is, or a
plant is.  The study of these and other small living things or organisms is called Microbiology.

What is a microbiology?
What sort of small, living things do microbiologists study?
All microbes are bad for us, aren't they?
How do microbes work?
What do microbes eat?
How small are microbes?
How do we see them if they are so small?
Are there any famous Microbiologists?  Go to Some Famous Microbiologists

When did microbiology start? Go to Early history of Microbiology



What is a microbiology?

Micro means very small and biology is the study of living things, so microbiology is the study of very small living things normally too small tobe seen with the naked eye.



ActivityUsing Microscopes

The science of microbiology started with invention of the microscope and the English scientist, Robert Hooke, takes the credit for this.

Coxiella burnetii bacteria  © 1994, The Centre for Microscopy and Microanalysis

Visit these other exciting sites to learn more about Microbiology.
What is Microbiology?
Microbe World - Your Gateway to the World of Microbes This is a super site for children!
The Microbe Zoo Another great children's site.
Microbe! follow Sam Sleuth with his detective work to find out about Microbes.
Pfizer Microbes Site
Foundation for Microbiology The home of the Foundation for Microbiology, with links to experiments and projects
Access to Inner Space - Dive and Discover  Visit the seabed and see some unusual habitats for microbes.
Pictures of microbes More pictures here.
Microbes in Action
Microbe Image Gallery Plenty of pictures here.  See what microbes look like.

What sort of small, living things do microbiologists study?

First we need to understand the classification of all living organisms. We also need to understand the fundamental characteristics of different types of organisms.  As outlined in the classification, microbiology includes the study of:

bacteria(or Eubacteria) fungi(or Archaeobacteria)
protists archaea algae
However, there are other organisms that are studied by microbiologists and these cannot be classified as living by the conventional definitions.

Such organisms include:

Index of Microbiology - Glossary

Microbiology Glossary

All microbes are bad for us, aren't they?

No.  It is true that some microbes cause disease and others cause decay and damage to inanimate objects, but without microbes we would not be able to exist.  Microbes are everywhere and the more we look the more we find, sometimes in the most unlikely of places.

Our body is infested with microorganisms and most of them are essential for our survival.  They assist in food digestion in our digestive system, for instance.

Even microbes that cause decay are useful for they breakdown dead matter into simple chemicals, so the matter can be recycled and used by other - probably more complex - life forms.  Without the decay process, the world would soon be covered in dead creatures and plants.

Microbes have different functions for different purposes and to occupy different niches in the biology of the planet.  They have evolved when and where they had the opportunity, without any moral imperative.  But as humans, we find that some are useful to us and others are dangerous to us.  So we view them as either good or bad.

"Good" microorganisms include those that are necessary to maintain our environment, in a way that will support our existence.  Then there are our very own microorganisms that our body uses as part of its internal defense system, to fight infection from outside.

"Bad" microorganisms enter the body in a number of different ways, but most commonly by the respiratory and digestive system, or by damaged skin.  They cause problems to the body because they destroy body tissue and release toxic substances.  This upsets the normal running of the body, which has to divert energy to its internal defense system in order to fight the invader.

Microorganisms that cause disease include:

bacteria fungi protists viruses virions prions


For examples see Rainforest Diseases and the Bad Bug Book.

How do microbes work?

Firstly, it should be understood that all living things "work" in the same way at the most basic level.  There are certain structures and functions that are common to all living organisms.  Likewise all living things use similar chemical processes to work - this is known as organic chemistry.  One chemical element above all others dominates organic chemistry - carbon.  This has some unique properties that allow trillions of different chemicals to be made from a few chemical elements.  An account of why carbon is the basis of life is shown here.

Lets us look at some of the key structural and chemical components of living organisms in general and microbes in particular.

The Cell
All living organisms are made from cells.  They are the basic unit from which living things are constructed and the smallest part of an animal or plant that can function independently.   All cells have an outer coat or membrane that is resilient to the external environment.  It is tough and resists damage to the cell, physically, chemically and biologically.  It also provides a good internal environment with a boundary where life processes can be performed by the organic chemicals inside the cell.  The boundary is important, too, because that stops the contents of the cell from being dispersed.

Two types of cell structure exist Prokaryote and Eukaryote.

Prokaryote structure 

Prokaryote cells lack a nucleus, and consist of a cell membrane in which several distinct components function.  Typically these are:

Chromosomes - A coiled strand of DNA
Ribosomes - Factory-like elements of a cell, where messenger RNA is turned into proteins - building blocks and enzymes - the cell needs

Cytoplasm - The general cell contents

Glycogen granules - to provide energy

Prokaryotes often also possess flagella, which help them move.

Eukaryote cells have additional internal components, notably a nucleus and mitochondria.

Nucleus - Contains the cell's DNA in threads of chromatin
Mitochondria - the cells' powerhouse where energy is released by aerobic respiration

Choroplasts - cells that contain pigment, such as chlorophyll, which may play a major role in producing food for the cell.

Plastids - A tiny structure within a plant cell that performs a particular function.  Apart from the nucleus, plastids are the largest components in the cell.They may containing pigments in which case they are called chromoplasts, or they may be colorless (leucoplasts).  They can changes from one type to the other.  Both the mitachondria and the chloroplasts in plants are types of plastid.

Chloroplast                                            Mitochondria
© 1999 The Centre for Microscopy and Microanalysis

Dictionary of Cell Biology

The origins of Mitochodria and Chloroplasts

Ribonuclease Single Crystal  © 1995-2000 by Michael W. Davidson and The Florida State University.

Enzymes are organic catalysts which speed-up an organism's chemical reactions, without changing themselves.  Chemical reactions can often be speeded up by heating, but in the case of living organisms this can damage them.  The enzyme, which is usually protein with a specific shape for each purpose, controls the chemical reactions in the cell and thus allows the organism to metabolize.

There are two groups of enzymes: intracellular and extracellular.  The former exist inside cells, controlling the metabolic rate.  The latter are produced by cells, but work outside of these.  For instance, digestive enzymes are used by the body to break down food in the digestive system.

Enzymes speed up reactions, without being destroyed by the reaction itself.  They  will not work in high temperatures, or at the wrong pH balance.   Each enzyme has a specific function, but it can work in either direction of the chemical reaction.

Chemical enzymes may be used repeatedly almost indefinitely, however organic enzymes do need to be replenished by the organism at intervals.

DNA, deoxyribonucleic acid, is a complex molecule containing instructions for all the functions of the cells of an organism, its "genetic information".  It replicates itself by separating its two interwoven strands (the helix) like a zip fastener and attracting free nucleotides (simpler molecules of nucleic acid) in the same order as the original.

The DNA molecule is a double helix made of four types of nucleotide.  These are aligned in a ladder formation, which is twisted like a screw.  On opposite sides of the double helix are companion nucleotides.  Adenine (A) and Thymine (T) are always located opposite other, and so are Guanine (G) and Cytosine (C).  So, each strand of the double helix is a "mirror image" of the other.  This is why A, T, G and C are the four letters associated with the genetic code.

DNA is the "master copy" for all the instructions for the cells of the organism.

The image shows the double helix structure of the DNA, which consists of two strands with the cross links at intervals joined be hydrogen bonds.  There are ten crosslinks for every complete twist of the double strand.  The lower image shows a section of the DNA helix, untwisted.  It shows the main components of the strand: Sugars (pentagonal shapes), phosphates (spheres) and organic bases (A, C, G and T).

To replicate, the DNA unzips along the center of the rungs of the ladder.  The exposed free ends can then form two new DNA strands by allowing "partner" molecules to link at the exposed rungs.  A can only pair with T, and C with G.

Sometimes the replication process is not perfect.  Stands break, or additional pieces of DNA become inserted, for instance.  This is how mutations occur and evolution happens.

For more information on Enzymes and DNA visit:
Demonstration of Cheese-Making Enzyme Magic

Enzyme Grabbers

A Model of a Bacterial Plasmid

Amino Acids Glossary

DNA image

An Introduction to DNA: A Project Design

DNA Replication

DNA Molecule - Two Views

DNA Extraction Lab by Joseph Windham

Extraction of DNA from Onion

DNA Extraction from Escherichia and coli cells


RNA, ribonucleic acid, is a much smaller molecule than DNA, which copies the information and takes part in the process of protein synthesis in cells.   It differs from DNA in that Uracil (U)replaces Thymine.   Unlike DNA it can interact with other molecules, specifically ribosomes.    The RNA copy of the DNA information is transcribed from the DNA template, this is known as transcription RNA, this is the copied message of the DNA.

mRNA, messenger RNA, is a further copy of the RNA transcript which has been spliced and modified.  It carries the information from the DNA which specifies an amino acid sequence of proteins.  In a eukaryote it then moves out of the nucleus into the cytoplasm, where it attaches to the ribosome.  In a prokaryote, which does not have a nucleus wall, the next process takes place on-site.  mRNA is the new message of instructions from the DNA.

tRNA, transfer RNA, is the adapter molecule which allows the mRNA nucleotide sequences to be translated into protein amino acid sequences.  The tRNA anticodons link up to their corresponding codons of the mRNA, one at a time, as the mRNA moves through the ribosome.   This is translation tRNA is the receiver of the message.

rRNA, ribosomal RNA, occurs with proteins to make up the ribosome which provides the site for translation to occur.  Ribosomes can be be located in clusters, or as free individuals, depending upon the final purpose of the altered proteins.  Ribosomes are the "factories"  that use the message to make essential chemicals for a cell to function.

Chromosomes and Genes are very long thread-like structures in the nucleus of eukaryotic cells, that carry the hereditary information of the cell.  They contain a long length of double-stranded DNA coiled up - the famous Double Helix, along with some RNA and special proteins.  Bacteria or prokaryotic cells, only have one chromosome each, which is not in the nucleus.

Genes are units or factors of inheritance, each one being a length of DNA containing a particular instruction.  For instance your eventual height is determined by a particular gene.

Aerobic and Anaerobic Respiration and Fermentation
Plants and animals are strict aerobes, which means they need oxygen to respire.  In simple terms aerobic respiration is breathing using oxygen.  Aerobic respiration in the cell is a chemical reaction whereby organic compounds such as glucose, are converted into energy for the cell, using oxygen from the environment as the final electron acceptor (linking to hydrogen).  The by-products of carbon-dioxide and water are released back into the environment.  (When plants photosynthesize they use light for their energy and to fix carbon for their own use from the carbon-dioxide, releasing oxygen as a by-product).

(Above right) Campylobacter: aerobic, gram-negative bacteria that can cause food poisoning.   © Neal Chamberlain
Anaerobic respiration by contrast is a process whereby respiration takes place without oxygen. This occurs only in some groups of bacteria, living in anaerobic environments such as in soil and stagnant water.  These strict (obligate) anaerobes use a substance other than oxygen - eg. sulfate, nitrate, carbonate - as the final electron acceptor.
(Above left) Clostridium difficile anaerobic bacteria that can infects the large intestine.    © Neal Chamberlain
(Right) Escherichia coli is glucose-fermenting Gram-negative bacteria
© 1994, The Centre for Microscopy and Microanalysis
Facultative anaerobes, such as yeasts and many bacteria, can use either fermentation or aerobic respiration depending on the availability of oxygen.  In fermentation the cell uses an organic molecule, such as ethanol or lactate, as the electron acceptor.  In the case of alcohol fermentation, carbon-dioxide is released.   Fermentation is less productive than aerobic respiration as an energy source for cells.   (When animal muscle tissue is required to function without an adequate oxygen supply there is a build up of lactic acid, which is an example of lactic acid fermentation - this does not release carbon-dioxide.)

Comparison of relative efficiencies of different types of respiration:

Aerobic respiration:
C6H1206 + 6O2 > 6H2O + 6CO2 + 2880 kJ
sugar + oxygen > water + carbon dioxide + energy

Anaerobic respiration with ethanol formation (alcohol fermentation):
C6H1206 > 2CH3CH20H + 2CO2 + 210 kJ
sugar     >   ethanol  + carbon dioxide + energy

Anaerobic respiration with lactic acid formation (fermentation):
C6H1206 > 2CH3CH(OH)COOH + 150 kJ
sugar >   lactic acid + energy

For more information use the on-line glossaries for Glycolysis, ATP, Krebs Cycle and Calvin Cycle

Index of Microbiolgy - Glossary
Microbiology Glossar

Types of association between and among life forms:

Symbiotic - a relationship between two different species of organisms, living together in direct contact.

Mutualistic - a relationship between two symbionts that is of mutual benefit, eg lichen (which is not an individual organism but the symbiosis of cyanobacteria and a fungus).

Commensal - a symbiotic relationship which benefits the symbiont , but has no effect on the host, eg many of the bacteria living inside and on the surface of the human body.

Parasitic - absorbing nutrients from a living organism the symbiont benefits, but harms the host - endoparasites live within the host, eg tapeworm ectoparasites live outside the host, eg  flea.

Saprophytic - absorbing nutrients from dead organic matter and decomposing it in the process, eg methanogens - an anaerobic sub-group of archaebacteria, used as decomposers for sewage treatment.

Host & Symbiont:

Host - participant which is exploited by the symbiont.
Symbiont - participant living in or on the host.


Bread mold spores © 1994, The Centre for Microscopy and Microanalysis

What do Microbes Eat?

Microbes have many different ways of metabolizing - getting the energy they need to live, known as nutrition.

Nutrition means the way an organism acquires two resources - energy and carbon - with which it synthesizes organic compounds for it to function, grow, and repair itself.  If the species uses light as its energy source it is called a phototroph, if it uses energy from chemicals it is a chemotroph.

Autotrophs are organisms that only require inorganic compounds such as carbon-dioxide for their source of carbon.

Heterotrophs are organisms which require at least one organic nutrient from organisms, or their by-products, as a carbon source for producing their own organic compounds.

According to their sources of carbon and energy, bacteria can be divided into four major groups: photoautotrophs, photoheterotrophs, chemoautotrophs and chemoheterotrophs.

Photoautotrophs are photosynthetic bacteria and cyanobacteria which build up carbon-dioxide and water into organic cell materials using energy from sunlight.  One product of this process is starch, which is a storage or reserve form of carbon, which can be used when light conditions are too poor to satisfy the immediate needs of the organism.   Photosynthetic bacteria have a substance called bacteriochlorophyll, live at the bottom of lakes and pools, and use the hydrogen from hydrogen-sulphide instead of from water, for the chemical process.  (The bacteriochlorophyll pigment absorbs light in the extreme UV and infra-red parts of  the spectrum which is outside the range used by normal chlorophyll). Purple and green sulfur bacteria use light, carbon-dioxide and hydrogen-sulphide from anaerobic decay, to produce carbohydrate, sulfur and water.  Cyanobacteria live in fresh water, seas, soil and lichen, and use a plant-like photosynthesis which releases oxygen as a by-product.
Cyanobacteria Lyngbia © 1997, Microbial Diversity


Photoheterotrophs use light, but obtain their carbon in organic form.  Only certain types of prokaryotes can do this.  The first life on Earth may have been of this type, using organic material such as amino acids not produced by biological activity.

Chemoautotrophs  include many bacteria.  They use special chemical processes instead of sunlight to produce organic material from inorganic.  Usually compounds other than sugar are oxidized for the chemical process.  Colorless sulfur bacteria which live in decaying organic matter where they are unable to use sunlight, oxidize the hydrogen-sulphide given off, to form water and sulfur.  Iron bacteria, which live in streams that run over iron-rich rocks, oxidize the iron salts. Hydrogen bacteria can oxidize hydrogen with the formation of water.  Nitrifying bacteria are important for enriching soil with nitrogen in a form that can be used by plants.  (See nitrification and denitrification).

Chemoheterotrophs need organic molecules for providing energy and carbon.  They are most commonly bacteria, but also protists, fungi, animals and some plants.  Chemoheterotroph bacteria can be saprobes which absorb their nutrients from from dead organic matter, thus decomposing it,  or mutualists and parasites, which absorb their nutrients from the body fluids of living hosts. E. coli is a chemoheterotroph.


A saprophytic species of penicillium - mold on orange

Nitrification and de-nitrification: Most of  the ammonia from decayed animal and plant proteins in the soil is used by bacteria such as nitrosomonas and nitrococcus as an energy source.  This activity oxidizes ammonia to nitrite whereupon other bacteria, nitrobacter, oxidize the nitrite to nitrate in a process called nitrification.   Nitrate released from this process can be assimilated by plants through their roots and converted to organic form such as amino acids and proteins.   Animals, however, can only assimilate organic nitrogen by eating other animals or plants.

Some bacteria obtain the oxygen they need for metabolism from nitrate instead of oxygen.  This results in the denitrification process, whereby some nitrate is converted back to nitrogen and returned to the atmosphere.


The Food Chain or Food Web: is the process by which biomass is recycled.  This involves the movement or cycling of organic chemicals through the environment, ie the movement of carbon, nitrogen, oxygen and water, through plants, animals, fungi, bacteria, etc by respiration and metabolism.   For the processes involved, see Cycling Chemicals and Rainforest Ecology


Nanobacteria filaments x35000
© 1999 The Centre for Microscopy and Microanalysis

How small are microbes?

Microbes are extremely small but how small?  They are so small that we cannot normally see them.  You could fit many thousands on this full stop  .

Let us consider a typical bacterium.  How big is it and what would it weigh?

It would be something like 0.003 mm long and it would weigh 0.000000000001 grams

Viruses are even smaller and recently nanobacteria a hundred times smaller than common bacteria, have been found.  At the other end of the scale, giant bacteria are known.  One, Epulopiscium fishelsoni is 0.06 mm long and 0.008 mm wide.

Now visit the Size comparison page.


How do we see them if they are so small?

We use microscopes to see individual microorganisms, but it is possible to see colonies with the naked eye.  Yeasts and molds are easy to see, as are the matted strands of algae.   But in such instances you will be looking at thousands of individuals.

How to see microbes. It is possible to detect individual microbes with the naked eye by employing a little trick.  Look at a well-lit blank space - the sky or a white wall, for instance.  Close one eye and partly close the other.  De-focus and you should be able to see faint stringy strands on the surface of the eye that look like beads.  Some of these are almost certainly bacteria such as streptococci.

QX3 Computer Microscope


Space Station Biomedical Lab


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