The Earth Life Web, An Introduction to Bacteria

The Bacteria
Unseen Miracles of Life
Bacteria are microscopic organisms, single-celled creatures which live mostly on the
surfaces of objects where they grow as colonies. Bacteria are very important both to the
world as a whole and to mankind in particular. Bacteria are important in making soil,
feeding cows, controlling insects, making medicines, making bioplastics, making plants
grow, degrading pollutants such as oil and plastics as well as in causing disease.
Microbiology is a huge and growing industry and even if you never intend to study
microbiology any further than these pages it will be good for you to have some
appreciation of the roles bacteria play in all our lives. Studying something you cannot
see, something which is not pretty, colourful or cute in any form is perhaps a more
cerebral activity than many people would like. Bacteria are, however, amazing creatures
and I have attempted to make the information here as much fun and as interesting as
possible. I hope that this will allow you to experience a little of the amazement bacteria
stimulate in the many people who study them. However by the very nature of their small
size and the limitations this puts on us when we studying them much of the information is
a bit dry and chemical. I apollogise for this.

Bacteria are one of the most ancient of living things and scientists believe they have been
on this planet for nearly 4,000 million years. During this time they have acquired lots of
fascinating and different ways of living. They also come in a variety of shapes. The
simplest shape is a round sphere or ball. Bacteria formed like this are called cocci
(singular coccus). The next simplest shape is cylindrical. Cylindrical bacteria are called
rods (singular rod). Some bacteria are basically rods but instead of being straight they are
twisted or bent or curved, sometimes in a spiral - these bacteria are called spirilla
(singular spirillum). Spirochaetes are tightly coiled up bacteria.
 Cocci Rods Ovoids Spira

Curved Rods Curved Rods Spirochaetes Filamentous

Bacteria are friendly creatures, you never find one bacteria

on its own. They tend to live together in clumps, chains or
planes. When they live in chains, one after the other, they are
called filamentous bacteria - these often have long thin cells.
When they tend to collect in a plane or a thin layer over the
surface of an object they are called a biofilm. Many bacteria exist as a biofilm and the
study of biofilms is very important. Biofilm bacteria secrete sticky substances that form a
sort of gel in which they live. The plaque on your teeth that causes tooth decay is a
biofilm.

Friends and Enemies

It is part of the human condition that we tend to be consciously aware of those few
bacteria that are pathogens whilst ignoring all those useful species without which life
would not be possible. It is important to realise that many, many more bacteria are
involved in interactions that are beneficial to the other party than in interactions that are
harmful. Some of these cause disease, but others help us digest our food. Many animals
are completely dependent on bacteria to digest their food for them, particularly
herbivores, large vertebrates like cows and sheep, to small invertebrates like termites and
collembola all are dependant on there comensal bacteria to stay alive. Further to this
bacteria are responsible for much good in medicine, they produce the best antibiotics and
with the help of modern microbiological techniques they can now be used to produce
many medically import products and even biodegradable planet friendly plastics
Most bacterial species are un-named and unidentified, tens of thousands of species have
been isolated, though they may not yet be allocated to a family or genera etc. There are
more than 15,000 known species of bacteria living in the sea. There are about 5000
named species of bacterium in 805 genera. The distribution is skewed with 397 genera
being monotypic, meaning there is only one species in the genera. This leaves an average
of 10 species per genus for the remaining 409 genera, however, only 89 genera have 10
or more species in them and nearly one third of all known bacteria (32.87%) are to be
found confined to just 16 genera. The most populous genus is Streptomyces with 509
species.

Note that the above information, and other taxonomic information used on this site was
synopsed from a pre 1998 1st edition of Bergey's Manual of Systematic Bacteriology.
Considerable forward strides have been made since then in bacterial taxonomy and the
new 2001 2nd Edition of the above manual is available from Springer-Verlag New York.

However it is worth noting that there are many distinct varieties of some species and the
concept of a species is sometimes a bit fuzzy. Also, and perhaps more importantly there
remain thousands of species of bacteria undiscovered and or unnamed. At the beginning
of this century Australian scientists looking at the bacteria in the stomachs of Kangaroos
for species that could produce acetates rather than methane from hydrogen and found
over forty species with this capability, half of which were completely new species as far
as science was concerned. This is just one example of the huge reservoir of unknown
bacteria waiting to be discovered. Some microbiologists claim there may even be more
species of bacteria than there are of insects. Insects are currently the most speciose taxon
known to man, at least in terms of named species with over a million known species.

The top 10 genera which contain 27% of all species are:

Genera Species No.
Bacteroides 65
Corynebacterium 67
Streptococcus 68
Mycobacterium 85
Lactobacillus 100
Mycoplasma 110
Bacillus 114
Pseudomonas 117
Clostridium 146
Streptomyces 509

It is a fact that bacteria live in a whole series of worlds which stretch our imagination, be
it the clouds in the sky, an Antarctic ice flow, a 100 degree C hot sulphur spring, 10 km
down at the bottom of the sea, 1500 m below the surface of the earth in solid rock, in a
rotting peach, in the roots of plants, the stomachs of animals and even your mouth,
bacteria can be found there. The way bacteria live and die is very different from our lives.
It is worth meditating on or even just day-dreaming about a life which can be as short as
15 minutes, which is often lived entirely in one spot less than 1/1000 of a mm across, and
where concepts like day/night, weather and up or down are meaningless.

Finally some bacteria, obviously, can live quite happily without light, however where
they are unique is when they are primary producers (like plants) and live without light.
They do this by reducing or oxidising various chemicals from Hydrogen through Iron and
Sulphur and a fuller description of this is available in Bacterial Life Strategies.

Strange facts and Bacterial Records

Bacteria really are found everywhere, from the tops of the highest mountains to the
bottom of the deepest oceans. In fact, some bacteria live way below the earth's surface
with many species inhabiting coal measures and subterranean aquifers.

Underground
The record for underground living goes to a species of Chemolithotrophic bacteria found
in Basalt deposits 1500m (4700ft) underground in solid rock. This really is solid rock,
scientists only learned about these bacteria when drilling for oil. Checking drill cores
brought up from these depths for signs of oil and found living bacteria.

The Sky
The air is full of bacteria. This is not surprising, when you realise that they are so small
you cannot see them with your naked eye it is not hard to accept that they should get
blown around easily. However it is not just surface bacteria getting caught up in the
breeze. Recent discoveries have shown that some bacteria spend their whole lives in the
atmosphere, growing and reproducing in the clouds above our heads.

On Ice
Bacteria are not as common in the extreme cold but they are there. Scientist know of
bacterial species that live all their lives in the ice of glaciers and other bacteria have often
found in the snows of the North and South poles Until recently scientists had thought
bacteria found in these latitudes were just blown there by the winds but in 2000AD they
proved that some of these species are different to any others and live at the North pole all
year round where the temperature varies between -17 and -85 degrees C. BRRRRRRR .
 Not So Cool
Not all bacteria like it cool, in fact some like it very hot. Hot
springs occur all around the world and where ever they do
Bacteria have learned to live in them. Some species are happy at
75 C while others think even this is cool. Species of Aquifex can
live in water as hot as 95 C, this is just 5 degrres away from the
boiling temperature of water. This is not the world record though,
that belongs to a species of Archaea which is happy to grow in
water around deep sea hydrothermal vents at temperatures as
high as 106 C (at these great depths, several miles down, the pressure stops the water
from boiling and keeps it liquid).

The Deep Sea

Anyone who has dived down into the water and felt
their ears pop knows that the pressure that water exerts
increases the deeper you go. Humans cannot go more
than a few tens of metres down without protecting their
ears and several hundred metres starts to cause
potentially lethal problems, even for experienced divers.
The oceans however are not hundreds, but thousands of
metres deep and the pressure increases by the equivalent of 1 atmosphere every ten
metres down. Thus bacteria which live at depths greater than 10000 metres must be able
to survive pressures in excess of 1000 times the air pressure at sea level. These bacteria
are called 'Extreme Barophiles'. Species that thrive at these depths are so biologically
different from sea level bacteria that they cannot function properly at pressures less than
400 atmospheres and die in a couple of hours if brought to the surface.

How Small??
Bacteria are small, on average most species of bacteria
have diameters of 0.5 to 2.0 microns. Obviously, though
diameter gives you a good indication of the size of a
spherical cocci bacterium you need to know its length as
well if it is a rod (cylindrical) bacterium. The smallest
bacterium have sizes down to 0.1 - 0.2 microns. Looking at it the other way, there is a
giant bacterium found in Sturgeon fish. This bacterium called Epulopiscium fishelsoni is
over 0.5 mm long.

Species Size in Microns

Epulopiscium fishelsoni 600x50
Bacillus megterium 4x1.5
Escherichia coli 3x1
 Streptococcus pneumoniae 0.8x0.8
Haemophilus influenzae 1.2x0.25
Rhodospirillum photometricum 30x3
Chromatium buderi 7x4

Fast Movers
Some bacteria can move. A few can glide across a
surface and some aquatic species can control their
buoyancy, and thus their depth in the water, through
internal gas vesicles (bubbles). Most bacteria however
move by means of one or more flagella (singular
flagellum). A bacteria that possesses one or more flagella
is termed 'flagellated' and there are 3 main different styles
of flagellation. If the bacterium has just one or two flagella placed at either one, or both
ends of its cell (this applies to rod and spirochaetic bacteria) it is said to have Polar
Flagellation. A bunch of flagella coming from one end of the cell is called Lophotrichous
flagellation (tufted) and if it the flagella come out at random points around the cell it is
called Peritrichous Flagellation. The flagella are not straight but are twisted in a sort of
wave shape. The distance between each wave crest or trough is fixed for a species and is
often important in identification. Bacteria move not by flexing their flagella the way a
fish flexes its tail and fins, but by rotating them like a propeller. This can enable them to
obtain speeds as high as 0.00017 kilometres per hour. This may not seem very fast, but to
put it into perspective remember that we are talking about very small organisms. Looked
at another way, they are travelling at about 50-60 body lengths per second. This would be
the equivalent of a 1.8 metre (6 feet) tall man running at 100 metres per second, 9 times
faster than the world record. Cheetahs, are the fastest animals on land but even they only
move at about 25 body lengths per second.

Representitative Bacteria
Type of Flagellation Bacterial Species
Polar flagellation Rhodospirillum centenum
Lophotrichous flagellation Rhodospirillum photometricum
Peritrichous flagellation Salmonella typhi

Cosy Living
Bacteria do not only live in extreme environments, but like us they are found in their
greatest numbers where the living is easy. Where it is warm and moist, with plenty of
easily obtainable nutrients. Anywhere that dead and decaying matter is present is a good
home for bacteria. So also is anything living. Bacteria live both on and in animals and
plants. Every human being has a particular flora of bacteria that inhabit every surface of
our bodies, on our skin, in our mouths, our stomachs and intestines etc. even in and
around our genitalia (see The Human Body as a Bacterial Environment).
 Small but Important
Bacteria are a major component of the unseen world of 'Micro-organisms' and as such
they play a decisive role in the maintenance of life on this planet. This life is not a static
process, instead it is a series of dynamic fluxes or flows. What is soil, becomes grass,
becomes a cow, becomes you and me and then becomes soil again. Bacteria, and other
micro-organisms are essentially important in the cycling of nutrients and energy,
particularly in the breakdown of dead organic matter to make the resources locked up in
things like dead trees available again to other living organisms. They also play a central
role and the fixation of atmospheric Nitrogen into organic molecules and in the cycling of
minerals such as Carbon and Sulfer. Further to this some bacteria also play an important
role in trapping the suns energy so that it can be used by living organisms. Any cycle or
system you look at has bacteria playing a crucial supportive role in it somewhere.
Bacteria are an essential in the maintenance of these flows of energy and nutrients
throughout our world. Without them the whole ecosystem would collapse.

Bacterial Ecology
Bacterial ecology is quite a large subject and here I have only presented a brief outline of
the more central aspects not covered in other parts of this chapter.

Energy
All organisms need energy. We get our energy from the food we eat, in other words from
organic matter. All other animals are the same. Plants and some of the Protista get their
energy from the sun. Various species of bacteria do both these things. When an organism
gets its energy from the sun we call it a 'Phototroph' from the Greek works 'photo' for
light and 'troph' meaning to feed. Literally this means 'light eating'. Organisms which do
not get their energy from the sun get it from the energy already stored in chemicals.
These organisms are called 'chemotrophs' meaning chemical eating. Most bacteria, and
Protists as well as all animals and fungi are chemotrophs. If the food chemicals are large,
complicated molecules of organic origin (ie they were once organisms), then we call the
bacteria and all the other animals that eat them 'Chemoorganotrophs', but if the molecules
are small and inorganic (ie iron, sulphur, hydrogen sulphide, etc) we call the bacteria
which eat them 'Chemolithotrophs'. Only bacteria are chemolithotrophs, whereas animals,
fungi and many protozoa are all chemoorganotrophs. Chemolithotrophic bacteria are
unique in our world, and because they require special adaptations to gain their energy
they are quite different to the more common chemoorganotrophic bacteria.

Some Long Words to Remember

Phototrophic = Getting energy from the sun
Chemoorganotrophic = Getting energy from organic molecules
Chemolithotrophic = Getting energy from inorganic molecules
Autotrophic = Able to live with CO2 as the only carbon source

Ecologically Important
Bacteria are important in soil formation, not only through the breakdown of organic
matter in already easily recognisable soils, but also in the conversion of rock to soil. Any
organic matter, however small a particle, is attractive to bacteria. The bacteria which live
by degrading organic compounds are called Chemooganotrophs. The carbon dioxide
produced during respiration by chemoorganotrophic bacteria is converted to carbonic
acid which is an important agent in the break down of rocks.

Bacteria also live in aquatic environments - ponds, streams, lakes, rivers, seas and oceans.
In many aquatic environments cyanobacteria, sometimes called Blue-Green Algae
because of their colour, are the most important primary producers. They contain
chlorophyll and trap energy from the sun in the form of light. In the depths of the sea,
miles below the surface where there is no light bacteria can still be the primary producers.
Only here they derive their energy from oxidising or reducing naturally occurring sulphur
compounds. In certain places in the ocean are upwellings of warm, minerally enriched
water called Hydrothermal Vents. They occur where the earth's crust is spreading.
Around these vents live strange communities of organisms including giant Pogonophoran
worms, giant clams and various other invertebrates. As no light ever reaches these areas
all the energy for life comes from the heat and mineral content of the water. The first step
in this process are the bacteria, either free living or living as partners (symbiotically) with
the worms and the clams.

Some Come With Extra Bits

As mentioned earlier many bacteria are regularly shaped (cocci, rods etc.), but this is not
true of all bacteria. Some have unusual appendages or attachments like long stalks or
tubes and these are called appendaged bacteria. Sometimes these appendages are used in
reproduction, sometimes they help the bacterium stick to a surface so it can stay where it
wants to be, and sometimes we do not know yet what they are for.

These various shapes are general indications only - as with all things in nature there is
really a vast continuum of shapes varying between these various central forms, some
bacteria are half way between a rod and a coccus, or only slightly curved.

Some bacteria have other appendages which are much smaller than those mentioned
above. These come in two sorts neither of which are very well understood from an
ecological point of view though they both look like fine hairs sticking out from the
bacterium in scanning electron microscopes images. One sort are called fimbriae (singula
= fimbria) which are much shorter than flagella and often much more numerous.
Scientists think that they may help the bacteria to cling to surfaces. The second sort are
called pili (singular = pilus), they are slightly larger than fimbriae and only occur in ones
or twos on any given cell. They are believed to be involved in conjugation, an aspect of
Bacterial Reproduction.

Finally, many bacteria secrete a layer around themselves which is made up of

polysaccharides with a few proteins. The resulting layer is quite variable between species,
being thick or thin and/or rigid (solid) or flexible (runny). If it is rigid it is called a
capsule and if it is flexible it is called a slime layer. These layers help bacterial cells bind
to surfaces, resist predators and retain moisture.

Surviving the Bad Times

Some bacteria, notably species of soil bacteria such as Bacillus and Clostridium, can
form a dormant, highly resistant form called an endospore. An endospore is formed
inside the normal cell and contains copies of all the cell's DNA. Endospores are inactive
and are used by bacteria to survive times when the environmental conditions do not allow
for normal living. In this way they are a bit like seeds, except that one bacterium can only
become one endospore.

Endospores can survive a very, very long time. In 1981 some spores stored in 1947 were
successfully germinated showing that they can survive for at least 34 years. More
recently, some scientists have claimed to have found viable (capable of germinating)
endospores from the bottom of a lake in Minnesota which are 7000 years old. Even more
amazing, in 1995 a group of scientists claimed to have grown bacteria from endospores
taken from the gut of a bee trapped in amber 25-30 million years ago. Finally in the year
2000 scientists grew some bacteria from endospores 250 million years old. This remain to
be checked by other scientists, but if it is true then it means that endospores might one
day be found and revived from bacteria which lived with the dinosaurs, the trilobites or
even earlier.

How Bacteria Eat

Like all living organisms bacteria need to eat in order to live, grow and reproduce.
However, bacteria are far too small to have a mouth. Instead they have special channels
in their cell walls and cell membranes which allow, or even assist some molecules to
cross. Once the molecules are inside the cell they can be broken down into their
componant parts before being rebuilt into the macromoloecules the bacteria needs in
order to buils and repare itself, or generate energy. Unfortunately for the bacteria the
surrounding environment is not always full of free-floating molecules of the correct sort.
Instead, the molecules may be all bound together in tissues such as a dead leaf or you or
me, or even our half digested dinner in our intestines. To solve this problem bacteria have
evolved the habit of leaking enzymes out into the environment around around them.
These enzymes then do what ever it is they do, attack specific tissues and molecules
(proteases attack proteins, cellulases attack cellulose etc) and break them up into smaller
units. Eventually molecules of a size that the bacterium can take into itself are madse that
the cell can then absorb them through the channels mentioned above.

Reproduction in Bacteria
Bacteria live strange lives. In optimal conditions they can reach maturity in 20 minutes,
they can then reproduce and one becomes two. twenty minutes later two becomes four. In
another twenty minutes they become eight. After the first hour there are 8. After two
hours there are 64. If the first bacterium fell into a perfect soup at the stroke of midnight
there would be 2 097 152 of them by the time you woke up at 7.00 am. By the time you
had morning coffee or recess at 10.40 am there would be 4.4 billion (that is 4.4 British
Billions or 4.4 million million = 4 294 967 296 bacteria). The numbers just keep doubling
every twenty minutes and they get horrendously large and my old bacteriology teacher
assures me that in 48 hours they total weight of all the bacterial offspring of just this one
bacterium would weigh 400 times the weight of the planet earth. If this seems
unbelievable experiment with the maths, the power of doubling is incredible. In 45 hours
the bacteria would only weigh 78% of the earths weight but a mere three hours later they
would out weigh it 400 times. Fortunately for us, bacteria never actually end up in a
perfect soup. In real life a cell normally takes between 1 and 24 hours to reach maturity.
In extreme conditions where there is very little food, or low temperatures it can take
much longer still, which is good for us. Also, many things eat bacteria or cause them to
die, which is why we aren't swimming in a soup of bacteria. Still it is worth remembering
how quickly one bacteria can become many when it finds something it likes to eat.

The simplest form of bacterial reproduction is called binary fission. Basically, this is
where a bacterium grows to about twice the size of the smallest bacterium and splits in
two. There is a little more to it than that, first the DNA in the cell makes a copy of itself.
The two copies separate in the cell and the cell grows two new cell membranes and two
new cell walls through its middle, effectively cutting the cell in half, to make two cells.
This is asexual (the 'a' in front meaning without) reproduction because both the daughter
cells have exactly the same DNA as the original cell and only one cell is involved. With
this sort of reproduction you can start a population with just one bacterium.

Sexual reproduction, like that used by most animals and plants involves at lease two
individuals and normally these are called males and females. Bacteria are not quite the
same as the higher animals but they do transfer DNA from one individual to another and
they can have a sort of sex.

Some methods of DNA transfer between cells seem almost accidental. When one
bacterial cell dies and its cell wall is ruptured the contents are released into the
environment. This includes the DNA which may be complete or broken into bits. Other
nearby bacterial cells can absorb this DNA and add it to their own and in this way they
gain extra DNA, if the dead cells DNA codes for a property they do not have then they
have gained this property. Viruses which attack bacterial cells can also be the agents of
the transfer DNA from one cell to another.

Bacterial DNA is normally a single circular double strand. Many bacteria can also
contain smaller sections of DNA in the form of Plasmids. Plasmids are still circles of
DNA and they can that replicate themselves within a bacterial cell. They often give the
host cell extra abilities such as resistance to antibiotics or the ability to make a useful
enzymes. Some plasmids give the bacterial cells that possess them a sort of masculinity.
They cause the cell to grow special sex pili which reach out from the cell and attach to
other cells that they contact. They then pull the two cells together. Once their cell walls
are touching these plasmids reproduce copies themselves into the other cell. In doing so
they give the other cell the ability to generate sex pili effectively making the second cell
male as well. Sometimes this plasmid DNA becomes can become joined up with, or
incorporated into the normal bacterial cell DNA and then the whole cell DNA is
replicated into the other cell. This is called conjugation and it is as close to what we think
of as sex as bacteria get. Plasmids can also move to new bacterial cells when a cell dies
the same as ordinary cell DNA can as mentioned above.

Bacteria and Disease

Bacteria cause disease. Most of these bacteria, like those listed below make their
presence felt immediatley and may or may not result in death. Some people though, can
be infected with a bacterium that normally causes a disease and not show any harmfull
effects at all, people like this are called carriers. A sad example of this was Typhoid Mary
who was identified as a carrier for typhoid fever in 1906.

Some bacteria attack us in a manner that is not immediately painful in fact the pain may
not be apparent for years. The primary example of this is tooth decay. Tooth decay is
caused by dental plaque which is a build up of 4 main species of bacteria on the teeth
around the gums: Streptococcus sanguis, S. sobrinus, S. mitis and S. mutans. In later
stages, this plaque can also involve species of Fusobacterium, Borrelia and
Actinomycetes. Tooth decay results from the corrosive action of organic acids released
by the bacteria as they metabolise sugars in your food as part of their normal life.

Introduction
During the 1990s Tuberculosis was the single greatest cause of death in humans by a
bacterium. The World Health Organisation estimates that nearly 3 000 000 people each
year die from tuberculosis. Respiratory and Diarrhoeal diseases cause a similar amount or
even more deaths but only some of these are caused by bacteria, others being caused by
viruses, protozoa and fungi. Apart from these diseases, Aids, malaria and the various
forms of Hepatitis all kill between 1 and 3 million people each year, but none of these are
caused by bacteria either so I will say no more about them here.

As scientific research and WHO immunisation programmes continue some of these

diseases are being brought under control and the toll on human life is decreasing. Others,
like AIDS, are still on the increase. Environmental disasters such as flood, draught and
earthquake, etc, increase the death toll from disease by making people more vulnerable
through shock, weakness and reduced sanitation. War, for similar reasons, increases the
incidence of disease. All in all, during the year 2000, bacterial diseases will probably
have killed 5 million people which accounts for only 10% of the 52 million human deaths
occurring on average every year. This is a huge number of our fellow human beings
dieing, however it is trivial compared with the number of people who will suffer some
form of illness or other caused by bacteria even though they are not killed by it. Bacterial
and other infectious diseases are far more significant in third world countries, a direct
result of poverty reducing sanitary practices, medical care and awarness. In more
developed countries, like the USA or the UK, Heart Disease and Cancer are responsible
for more than 70% of deaths.
 How Do Bacteria Cause Disease?
The first thing the bacterium has to do is enter your system. We come into contact with
millions of bacteria every day. They are in the air we breathe, in and on the food we eat
and on the surfaces of most things we touch. Apart from our normal flora, bacteria that
come into contact with us have to pass our various defence mechanisms, our dry skin and
our acid stomach. Physical actions such as the movement of matter through our
alimentary canal, brushing our teeth and washing all help to make life difficult for
bacteria. Those bacteria which do colonise our system generally do so by breaking
through the mucus barrier that lines most of our alimentary canal (mouth to anus), or
entering through damaged tissue, ie wounds and bites, etc.

Once a bacterium has entered the system it is free to grow and spread - nearly all
infectious diseases start out as small localised infections and will only spread through the
system if the bacteria gain access to the blood stream.

Infection simply means the bacterial or other agent entering the system. It does not equate
with disease or damage. You can be infected by an organism that never makes you ill. An
infectious agent is simply an organism that is capable of getting past your defences and
then living/growing inside or you.

Bacteria rarely, if ever, cause disease merely by being present, even the virulence factors
they produce to help them invade the body often do little real harm.

Virulence factors are normally enzymes. Their role is to make it easier for the bacterium
to invade your body. A good example is 'hyaluronidase' an enzyme secreted by a number
of bacteria that breaks down hyaluronic acid, a sort of organic cement that holds the
different tissues of your body together. By destroying this cemment bacteria can make a
passage for themselves through your tissues.

The pathogenicity of invasive bacteria, or their ability to cause disease is generally the
result of toxins. Substances produced by the bacterial cell, sometimes simply as a by-
produce of its normal metabolism, which interact negatively with our body, by interfering
with the normal functioning. This is often done by simply damaging the specific cells,
blocking the transmission of some sort of internal signals or other or by overstimulating
some sorts of cells so they malfunction. The ecological reasons for the production of
these toxins is not always understood. Also, because of the vagaries of bacterial genetic
reproduction, otherwise harmless species can acquire a gene which causes them to secrete
a toxin, thus making them a pathogenic strain of a normally harmless species. A good
example of this is Escherichia coli which lives harmlessly in most people's intestines but
which occasionally makes us sick.
Toxins that are leaked or secreted out of the bacteria cell and into its host (you and me) is
called an Exotoxin. An Exotoxin that is secreted in the intestines is called an Enterotoxin.
Bacterial cells can also produce substances which, though toxic, are not secreted into the
host but remain bound to the bacterial cell wall. These substances only fulfil their toxic
potential if and when the bacterial cell dies and is lysed (broken open and its contents
released).

Exotoxins come in three different forms called cytalytic toxins, A-B toxins and
superantigen toxins. Cytalytic toxins work by causing lysis of host cells thus damaging
tissue. A-B toxins are two or more molecules working as a team. The A molecule binds
to a cell wall where it forms a channel to allow molecule B access to the cell.
Superantigen toxins work by overstimulating the body's immune response system.
Diphtheria is a cytalytic toxin. Tetanus is an A-B toxin. Cholera is an A-B toxin that is
also an Enterotoxin because it works in the intestine. Cholera toxin works by disrupting
the ionic balance of cells' membranes which results in the cells of the small intestine
secreting large amounts of water into the intestine. This keeps happening and has two
effects; all the water in the small intestine causes diarrhoea and thus the body dehydrates.
Eventually the small intestine loses water faster than the large intestine can reabsorb it
and death follows from dehydration.

Endotoxins are generally much less pathogenic than Exotoxins and rarely cause death.
Many fevers are caused by endotoxins whereas exotoxins never produce a fever.

Clostridium botulinum produces toxins which are among the most poisonous or toxic
substances known. One milligram of pure Botulinum toxin is enough to kill 1 million
guinea pigs.

Bacteria and Technology

 Introduction
Unknown to many people, bacteria play an important role in many technological fields,
mainly in mining, medicine, food culture, plastics synthesis and sewage control. The
overall commercial worth of bacteria in these operations is immense. It is also fascinating
to see how much of a hidden effect bacteria have on our lives. One way bacteria are
useful to mankind is in the production of complex organic molecules that are of used in
small amounts as part of the our normal process of living, these include antibiotics,
vitamins, amino acids and enzymes. By manipulating the genes of the bacteria and
esuring they have ideal living conditions scientists can make the bacteria concentrate
almost exclusively on producing just one chemical. These bacteria are then grown in
special fermenting vats where the end product can be as much as 80% dry weight of the
desired chemical. The desired chemical is then separated from the bacteria and made
ready for commercial or practical use.

Bacteria have also been pivotally important in the study of genetics and genetic
engineering but this is a separate and complicated subject which I am not going into here.

Mining
The bacterium Thiobacillus ferrooxidans is the important organism here. It works by
catalysing the oxidation of metal sulphides, particularly copper sulphate so that they are
soluble in water ie, Cu2S to 2Cu2+ and SO42-. This allows the copper to be leached out of
the rock. The copper is then precipitated (brought out of solution) as a solid by passing it
over iron. Copper sulphate will oxidise naturally in the presence of air in an acid
environment, but only slowly. The presence of T. ferrooxidans speeds up the process by
over 100x. This allows miners to extract metal from low grade ores in a relatively
ecologically friendly way. T. ferrooxidans is also used in the organic leaching of gold and
uranium with the help of other bacteria such as T. thiooxidans and Leptospirillum
ferrooxidans. The mining of gold like this in small enclosed environmentally friendly
digesters is becoming more popular.

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 Antibiotics
Commercially, antibiotics are the most important of these substances (called secondary
metabolites). An antibiotic is a substance that suppresses the growth of micro-organisms
such as bacteria and fungi, and they are produced by some bacteria to prevent other
bacteria from growing near them and using up their food. Over 8000 antibiotics are
known to science, but we are always looking for more and currently (2000 AD) about
200-300 more are discovered each year. Antibiotics are used to treat diseases caused by
bacteria or to prevent these diseases from occurring in the first place. The following list
gives the most important antibiotics produced by bacteria. Penicillin is not on the list
because it is produced by a fungus called Penicillum chrysogenum.

Antibiotics produced by Bacteria

Antibiotic Bacterial Species
Tetracycline Streptomyces remosus
Streptomycin Streptomyces griseus
Cyclohexamide Streptomyces griseus
Neomycin Streptomyces frodiae
Cycloserine Streptomyces orchidaceus
Erythromycin Streptomyces erythreus
Kanamycin Streptomyces kanamyceticus
Lincomycin Streptomyces lincolnensis
Nystatin Streptomyces noursei
Polymyxin B Bacillus polymyxa
Bacitracin Bacillus licheniformis

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Vitamins
The vitamin industry is huge and commercially it is worth more than 1 billion USD per
year. Most of these vitamins can now be synthesised chemically in vats. Some, however,
are too complicated to be produced in this way and are made biochemically. The most
important of these is vitamin B12. Vitamin B12 is essential for normal living in all
animals and a deficiency of it causes a disease called pernicious anaemia. Commercially,
vitamin B12 is produced by several bacteria, the most important of which is
Pseudomonas denitrificans. Other important producers are species of the genus
Propionibacterium. The other important vitamin made commercially by micro-organisms
is Riboflavin. Most riboflavin is produced by a fungus called Ashbya gossifyii, however,
bacteria are used to produce some as well.
 Amino Acids
Amino Acids are used in medicine to treat dietary deficiencies and in the food industry as
antioxidants, sweeteners and flavour enhancers. Amino acids come in two forms one of
which is the 3D mirror image of the other. They are called the D and L isomers of a
particular amino acid. Living things use only the L isomer amino acids. Unfortunately,
chemical methods of production produce 50% D and 50% L isomers, so half of what is
produced is no use to anybody. Bacteria, however, being living things, produce only the
L form. This is one of the reasons that they are so important in this industry.

Perhaps the best known commercially produced amino acid is glutamic acid which is sold
as Monosodium Glutamate, MSG, a flavour enhancer. Two other important amino acid
products are aspartic acid and phenylalanine. Mixed together these two become the
popular sugar-free sweetener, Aspartame.

Lysine, another essential amino acid for humans, is also produced from bacteria, it is
used as a food additive to enhance its nutritional value. Lysine is produced by
Brevibacterium flavum whilst glutamic acid is produced by Corynebacterium
glutamicum. Over half a million metric tonnes of amino acids are produced commercially
each year, the table below lists a few with their uses.

Bacterially Produced Amino-acids Used as Food Additives

Lysine Nutritive additive in bread
Glutamate Flavour enhancer, meat tenderiser
Glycine Flavour enhancer in sweet foods
Cysteine Antioxidant in bread and fruit juices
Tryptophan and Histidine Antioxidant
Methionine Nutritive additive in soy products
Phenylalanine and Aspartic acid Sweetener in soft drinks

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Enzymes
Enzymes are proteins that make chemical reactions go. Enzymes allow bacteria to make
all the other useful molecules described in these sections. Of course, most of what you
and I are made of was built by enzymes as well so they are pretty important biologically.
Usually each enzyme has its own task which it does over and over and over again until it
wears out, such are the building blocks of life. As well as building things up, enzymes
can also break large molecules and groups of molecules down, such as the food we eat,
into smaller more easily used parts. Many bacteria produce enzymes which they secrete
into the world around them. These enzymes breakdown their target molecules outside of
the bacterial cell, which can then be absorbed by them (See 'How Bacteria Eat'). This is
useful for people who want to manufacture enzymes. Enzymes come in different types
such as Proteases which breakdown protein molecules and Amylases which breakdown
starch. Modern technology makes use of enzymes in many ways, you may even know of
some already. Proteases are used for spot removal in drycleaning, meat tenderising,
wound cleansing, desizing textiles and as detergents. While glucose isomerase is used in
soft drink manufacture and cellulases are used in genetic research and forensic science.

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Plastics
Plastic fantastic - plastic is everywhere in our modern society. It is ideal for producing a
variety of products such as containers for liquids of and all sorts other materials,
machinery and plates, tables, cups, etc. However, plastic is a nuisance when it is no
longer useful and is left lying around the countryside. Plastic is still a problem even if it is
buried in a landfill. The reason for this is that it is not biodegradable, in other words it can
not be rotted away by bacteria and fungi as is natures normal method of recycling the
materials. Chemically produced plastics are made of multiple units of molecules such as
Polypropylene, Polyethylene and Polystyrene, which most bacteria and fungi cannot
digest or breakdown. Thi means they are non-biodegradable, and so they last for years
once abandoned, an ecological waste and often an eyesore.

Plastics do not have to be a problem like this though, science has developed an answer.
The chemical giant ICI is manufacturing a plastic in the UK from multiple units of a
mixture of two bacterially produced molecules, Poly-B-hydroxybuterate and Poly-B-
hydroxyvalerate. These molecules make a polymer just like ordinary plastic but having
the essential difference that once left out in the compost or in a landfill they can be
broken down by bacteria and fungi to become part of the cycle of life again. In 1998 only
600 tonnes of this plastic was produced but in the future, mass production could make it
as cheap as ordinary plastics. Without doubt further research will reveal more microbial
plastics to help save the environment. Why not ask your local politicians what they are
doing to encourage the use of biodegradable microbial plastics. The picture (left) is a
shampoo bottle sold in Europe, it is made of microbial plastic. The bacterium which does
all the work is Alcaligenes eutrophas.

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 Vinegar
Vinegar is a common substance, used in pickles and other food stuffs. Its technical name
is Acetic acid and it is a small molecule made from Ethanol (the alcohol in booze) by a
number of species of bacteria. The bacteria actually make acetaldehyde from the alcohol
first so the reaction looks like this:

CH3CH2OH to CH3CHO to CH3COOH

The bacteria involved are called acetic acid bacteria and the two most important genera
are Acetobacter and Gluconobacter. Pure acetic acid can easily be made chemically, but
vinegar made from wine by these bacteria has its own flavour resulting from other
molecules present in the original wine. Vinegar is therefore made by bacteria rather than
in chemical vats.

Bacterial Classification
The taxonomy of bacteria is not very definitively worked out yet, especially the higher
levels of classification. Some authorities believe that the degree of variance between
different bacterial groups is sufficient to give them each 'Kingdom Status' of their own.
Thus in the 9th edition of "Brock: Biology of Microorganism" you will find reference to
13 Kingdoms of Bacteria. From the point of view of these pages it is not really important
whether you think of the different categories as Phyla or Kingdoms as long as you are
aware that the bacteria are an incredible diverse group of organisms. Here I have
 followed the classification scheme laid out in the 2nd edition of "Bergey's Manual of
Systematic Biology".

Gram Staining
You will find bacteria referred to as 'Gram +' or 'Gram Positive' and 'Gram -' or 'Gram
Negative' this is a reference to how the bacteria responds to the Gram staining method.
Staining methods are designed to make a staining agent bind to the cell wall of the
bacteria. The Gram staining method is named after Christian Gram who invented the
method in 1884.

In testing for gram stain response, microbiologists first spread some bacteria on a slide,
then fire it by passing the slide through a flame briefly. The next step is to flood the slide
with crystal violet solution for 1 minute. Then they add iodine solution for 3 minutes - at
this stage all cells are purple. Adding alcohol for 20 seconds results in Gram negative
cells becoming clear again, ie they lose their purple staining. Lastly, the cells are
restained with safranin. This results in gram positive cells remaining purple and gram
negative ones being red or pink. Gram staining is nearly always the first step in
identifying a new sample or species of bacteria. Nowadays, gram staining can be done in
one step using a fluorescent dye and a fluorescence microscope.

The Phyla of Bacteria (as used on this site and taken from Bergey's Manual of
Systematic Bacteriology 1st Ed.)
Name of Phylum Number of Species Number of Genera
Aquificae 27 12
Xenobacteria 29 11
Chrysogenetes 1 1
Thermomicrobia 13 6
Cyanobacteria 78 62
Chlorobia 17 6
Proteobacteria 1644 366
Firmicutes 2474 255
Planctomycetes etc. 13 5
Spirochaetes 92 13
Fibrobacter 5 3
Bacteroids 130 20
Flavobacteria 72 15
Sphingobacteria 76 22
Fusobacteria 29 6
Verrucomicrobia 5 2
 Phylum 1 - Aquificae
This is a small group of thermophilic to hyperthermophilic chemolithotrophic bacteria,
meaning that they derive their energy from inorganic molecules and they live in hot
environments. Members of the genus Aquifex can live at temperatures as high as 95
degrees C and they have an optimum growth temperature of 85 degrees C. Aquifex is an
aerobic bacterium but it can only tolerate low quantities of oxygen. Most of the rest of the
phylum are anaerobic and cannot tolerate the presence of oxygen at all. Aquifex utilizes
H2S or S2032- as its energy source.

Thermodesulfobacterium is another member of this group. As its name suggests, it is a

sulphur reducing bacterium, reducing SO42- to H2S. Thermodesulfobacterium likes it a
little cooler than Aquifex having an optimum growth temperature of 70 degrees C, and it
is anaerobic.

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Phylum 2 - Xenobacteria
This group comprises a number of aerobic chemoorganotrophic bacteria. The two best
studied genera are Thermus and Deinococcus. Thermus is a thermophilic bacterium. The
enzyme Taq DNA Polymerase comes from Thermus aquaticus. This is the major enzyme
used in Polymerase Chain Reaction (PCR) techniques for amplyfying DNA. The best
known Deinococcus species is D. radiodurans, so named because of its incredible ability
to survive high does of radiation. D. radiodurans can survive 30,000 Gy of ionizing
radiation (1 Gy =100 Rad). A human being can be killed by less than 5 Gy, making D.
radiodurans 6000 times better at surviving radiation than us.

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Phylum 9 - Planctomyces and Allies

Chlamydiaceae

Chlamydiaceae is the smallest of the the two families in this phyla , containing only 3
species all in the genus Chlamydia. All three are obligate parasites of warm-blooded
animals; C. trachomatis and C. pneumoniae of humans and C. psittaci of birds and
occasionally mammals, including humans. All are pathogenic. C. trachomatis causes
trachoma the leading cause of blindness in humans, as well as otitis, a non-gonococcal
urethritis, urethral inflammation, Lymphogranuloma venereum and cervicitis. C.
pneumoniae causes a variety of respiratory problems similar to pneumonia. C. psittaci
causes epidemic Psittacosis in birds, particularly parrots, as well as pneumonia, arthritis
and conjunctivitis in young mammals such as kittens, calves, foals and piglets.

Planctomycetaceae

This is another small but distinct group of bacteria. They are unique because of the stalk
that they produce, which unlike that in Caulobacter is made of protein. They are also
interesting because they are budding bacteria. The stalk is believed to be used as a means
of attachment to substrates. They are primarily aquatic aerobic chemoorganotrophs.
There are 4 genera and 10 species; Pirellula, Planctomyces, Gemmata and Isophaera a
gliding filamentous form. Little is known about the ecology of any of these genera.