Bacterium_1
Bacteria
Bacteria (singular bacterium) are minute organisms that often consist of single cells, like the rod-shaped cell shown above
which is about one thousandth of a millimetre (mm) in diameter (that is one micrometre or about a tenth the diameter of
one of your cells or about one thousandth the volume of a human cell), but may exist as filaments (chains of cells) or
cubes of cells or as large
'slime cities' or biofilms that may be easily visible to the naked eye. Many bacteria are now
known to alternate between single-celled swarmers that disperse to find new habitats, and colonies or 'cities' held
together by slime. The pictures above are 3D computer models produced in Pov-Ray.

Tech Level: This article includes foundation introductory material aimed at a wide audience, but the section on 'Transport
processes' is quite advanced and readers wanting a less technical account may wish to skip this section.

Bacterial Cell Shape

Bacteria come in a variety of shapes including: rods (bacilli), spheres (cocci), squares, star-shapes, coma-shapes and
long corkscrew-shapes.
Spirochaete
Above a single-celled helical or corkscrew-shaped bacterium, called a spirochaete. This resembles the bacteria that live
in thick mud, and those that cause diseases in humans such as Lyme's disease and syphilis. As they move they rotate
like a corkscrew, and this allows them to bore their way into thick mud, or into your tissues! These types can be quite long
cells, up to about one fifth of a millimetre in length, but it is quite narrow.

Bacteria are the simplest cellular lifeforms we know of. However, although a bacterial cell is much simpler than an animal
or plant cell, they are still extremely complex, especially on the nanoscale! The earliest recognisable
fossils are of bacteria which completely dominated the Earth 3.5 billion years ago! Bacteria resembling photosynthetic
cyanobacteria formed large layered structures, called stromatolites along the shores of the early seas. Stromatolites still
dominate in areas like the Dead Sea, but in the ancient Earth they were the dominant life-form! Bacteria like these
cyanobacteria generated the oxygen in the Earth’s atmosphere (early bacteria did
not require oxygen, and some still don’t and may even find it poisonous!). In many ways bacteria are still the
dominant life-form on earth today – there are more bacterial cells in your body than animal cells! (Although the bacterial
cells are much smaller). Bacteria are essential to every ecosystem as they transform and recycle chemicals and
elements, for example in the carbon, oxygen, nitrogen and sulphur-cycles. Inside your cells are
structures called mitochondria. These structures are dynamic, constantly fusing and dividing and being moved around
inside your cells, and they perform a vital function – they burn fuels like glucose to provide cells with usable chemical
energy packaged in ATP molecules. These mitochondria are the descendents of bacteria that entered the ancestral cell
billions of years ago! You are a composite organism since you are part bacteria!

Bacteria are generally considered to be single-celled organisms as those most closely studied historically were isolated
swarmer cells, like the one above. Swarmer cells swim, crawl, glide or drift around. However, bacteria also form
communities in which thousands of cells come together, held together by slime they secrete to form ‘slime cities’ or
biofilms. Within these communities the bacteria communicate with each other and work together, however they remain
separate as they do not generally form contact junctions with one another (as cells do in an animal or plant body) – it is
rather like many separate organisms working together as a single organism. In these biofilms, slime towers
(microcolonies) shed swarmer cells into the water stream above. Some bacteria develop to the next
stage of multicellularity and form chains of cells (filaments) in which neighbouring cells may communicate with each other
using electrical signals through special junctions. Some form minute fungus-like structures with fruiting bodies emerging
from a sheet of cells to release spores.
Why different sizes and shapes?

Bacteria come in a very diverse range of forms. They are neither plants nor animals, but belong instead to the prokaryote
kingdom. A minority of bacteria are
parasitic on other organisms, often causing disease. For example, tuberculosis,
leprosy, many stomach and bowl disorders (food poisoning) and syphilis are human diseases caused by bacteria.
Bacteria are distinct from viruses. Bacteria represent the simplest living cells we know of, however, they are still extremely
complex. Viruses are acellular or subcellular protein packages of infectious genetic material. Viruses are not capable of
independent life, but are parasites that must invade their particular host cell type, take control of the cell, and then use
the cell’s machinery to make more copies of themselves – viruses are pirates of the cell! Bacteriophages are viruses that
attack bacteria. Some bacteria are
photosynthetic, but most are (chemo)heterotrophs. Heterotrophs can not fix
carbon, as photosynthetic organisms can, but instead rely on pre-made organic carbon sources which they obtain from
other organisms. Some heterotrophs are parasitic but most simply absorb the dead and decaying remains of other
organisms - they are
saprotrophs. Saprotrophs secrete enzymes to digest dead and decaying organic matter which they
then absorb. Some are
commensals, which means they feed on the waste of other organisms whilst living on or inside
them but cause no harm to the host, for example, 55% of the solid part of human faeces is bacteria! There are 10^10 (10
billion) bacteria per gram (wet weight) of faeces! Finally, some bacteria can manage to make a living by simply eating
rocks! Rock-eating bacteria that can fix their own carbon without photosynthesis are called
chemoautotrophs.

First let us look at the variety of shapes and then let us link that back to how bacteria obtain nutritients by the methods we
have just described.

The most common bacterial cell shapes are:

1) rod-shaped (usually a cylinder with hemispherical end-caps), bacteria with this shape are called
bacilli (sing. bacillus),
e.g.
Bacillus subtilis, Escherichia coli, Salmonella typhimurium;
2) spherical (coccoid), bacteria with this shape are called
cocci (sing. coccus), e.g. Diplococcus, Streptococcus;
3) comma or vibrioid shaped (after the archetype example
Vibrio);
4) helical or spiral shape, an extension of the comma-shaped theme over more turns of the helix, e.g. spirochaetes;
5) filaments, either single and highly elongated cells or chains of cells;
6) flat cells, which may be discoid, triangular, star-shaped or square, common in salt-loving halobacteria, e.g.
Haloquadratum walsbyi has square-shaped cells 2-5 micrometres in diameter and 0.1-0.5 micrometres in thickness.
These cells adhere to one-another to form microcolonies comprising square sheets (about 40 by 40 micrometres) which
float in the water column. This shape probably enhances the interception of light utilised by these organisms.
7) A variety of other shapes also occur.
Bacterium_2
Above: a section through a single-celled rod-shaped bacterium. Shown in purple is the tough capsule or cell wall of the
bacterium (this is a type of bacterium known as Gram positive, but there are other structural types with different wall
arrangements). This capsule protects the bacterium. Shown in light blue is the
peripheral cytoplasm which is bounded
by a
cell membrane which you can just see underneath the capsule. The cytoplasm consists mostly of water and
proteins (including
ribosomes that manufacture other proteins). This membrane is similar to the membrane that forms
the 'skin' of your own cells, and is also made up of mostly fats and proteins. The central swirly region is the
nucleoplasm. The red threads are the DNA, because the nucleoplasm contains the genes and forms the central
computer of the bacterial cell. (Unlike animal cells, there is no nuclear membrane). Note that the bacterial cell has fewer
internal compartments than the animal cell.
Now, what about the long black coils? These are the engines of the bacterium and are called
flagella (singular flagellum)
which means 'whip' in Latin, which is a bit of a misnomer for bacteria because these flagella do not lash about but rotate
like corkscrews. These motors are very fast, but not as good as drilling into thick materials like what the spirochaete can
do by turning its whole body into a corkscrew!

If you look carefully at the roots where the flagella join the cell body, then you will see what look like little
wheels, indeed
that is exactly what they are, but instead of driving the cell along as do the wheels on a car drive the car along, they drive
the flagella and cause them to rotate like corkscrews, propelling the cell along. You may notice the flexible hook that joins
the flagellum to this system of wheels. We shall have a closer look at these wheels and hooks shortly. Note then, that
bacteria 'invented' wheels billions of years ago! Click here to see how these wheels work.

Why do bacteria use these 'corkscrews' to get about when larger animal cells use different propulsion systems (they may
crawl like the amoeba or use beating hairs called cilia or lash a long whip-like flagellum which does not rotate as does the
flagellum in bacteria but lashes from side-to-side)? Well, when one is as small as a bacterium, water starts to behave
oddly - it becomes thick and sticky (it has a high relative viscosity due to the system having a very low Reynold's number)
so the bacterium is effectively swimming through treacle. Now imagine trying to swim through treacle with a paddle, push it
to the left and you move forward a bit, but push it back to the right and you move backwards a bit - in short you get
nowhere, you just oscillate about a bit!

This does not happen in water because the water flows away, so you are not pushing the same water backwards and
forwards. This is expressed by what we call
time-reversibility. Reverse the motion of someone swimming with a paddle
and you can tell the difference because they go backwards! Now do the same to someone paddling in treacle and you
can't tell the difference. Now, to move forwards a swimmer has to break this
time-reversal symmetry so that the video
looks different when played backwards. A corkscrew is ideal for this, because a corkscrew is twisted either clockwise or
anticlockwise. Reverse a corkscrew and it does make a difference - try turning the corkscrew in the opposite direction
next time you open a bottle of wine. This is why a corkscrew can drill through thick materials like cork. Now, by using
corkscrew-like engines the bacterium overcomes the problem of its tiny size which makes water behave like treacle, and it
easily ploughs forward.

Before I get into more technical details of these rotary engines, let me just stress the importance of bacteria. Most people
think of them as germs, but the vast majority are not only harmless to humans, but beneficial. The Earth's ecosystems
would grind to a halt without bacteria, in fact
bacteria are the foundations of life on Earth, kill everything else but the
bacteria and life continues, kill all the bacteria and the Earth dies. Bacteria recycle nutrients into the biosphere, they
break-down dead animal and plant remains and do all sorts of wonderful chemistry. Some do cause disease, however.
Examples include most bouts of food-poisoning, tuberculosis, syphilis, hospital superbugs and others. However, they do
not cause all infectious diseases! Viruses, fungi, worms and other organisms also cause many diseases.

Killing all bacteria on Earth is easier said than done of course! Bacteria are extremely tough, partly because they can
reproduce so rapidly, the fastest double their number every 10-20 minutes in optimum conditions, and partly because
they are so adaptable - they evolve rapidly when they need to.

Did you know?

If a single bacterium (weighing ~10^-15 kg) doubled every 20 minutes, then the total population of bacteria would weigh
the same as about 10 000 Earth's after two days! Clearly this does not happen in Nature because conditions for bacterial
growth are seldom optimum - the bacteria may run out of food for one thing.

The appearance of
superbugs that are resistant to almost every known drug is testament to the ability of bacteria to
undergo rapid genetic changes and evolve and adapt to changes in their environment. There are even bacteria that grow
inside nuclear reactors! Humans often boast at how their nuclear weapons could sterilise their planet, but they can't, they
would just kill all the big creatures like humans. Sometimes it pays to be small - smaller creatures require fewer nutrients
and so can reproduce rapidly. Bacteria grow so fast because they are small and so can easily absorb nutrients and get
the food to all their parts, in contrast, larger animals require complex circulatory systems (heart and blood) and this limits
the rate at which food can be absorbed. By reproducing faster, smaller creatures evolve faster - imagine how humans
have changed in the past 10 000 generations (say 300 000 years), well bacteria pass through 10 000 generations in as
little as 20 weeks!

Click here to learn about
bacterial slime cities!

Transmission Electron Microscopy

The images below show (ultrathin) sections of a Gram negative rod-shaped bacterium (Bacteroides fragilis). Each cell is
about 1 micrometre in diameter. These cells have been chemically fixed. Click images to view full-size.
Bacteria_TEM
The diagram below shows some transmission electron micrographs of bacteria (taken by Bot). These are bacteria that
have been cut into sections some 70 millionths of a millimetre thick and viewed under a powerful electron microscope.
The bottom picture shows a close up view of one cell in the act of splitting into two new daughter cells. This is how most
bacteria reproduce. Can you identify the cell envelope (cell wall, which has 4 layers in this type of bacterium, which is
called the Gram negative type), the ribosome-rich peripheral cytoplasm and the central DNA-rich nucleoplasm?
Click here to see a labelled version of this diagram for the answers! Notice that the peripheral cytoplasm is granular (due
mostly to ribosomes) and in the central nucleoplasm you can see strands of DNA (with attached proteins). Notice that the
surface of this bacterium type appears somewhat 'hairy', actually in life these 'hairs' absorb water and form a slimy outer
layer. An additional and much thicker slime capsule may also form a sheath around the cell. The scale refers to the
enlarged image and shows that the width of each bacterial cell is about one micrometre or one thousandth of a millimetre
across. Notice that even this high magnification does not reveal most of the details of the complex nano-scale machinery
that exists within the cell.

The Nucleoid

The bacterial genome usually consists of a single circular chromosome of double-stranded DNA. However, some
bacteria possess multiple circular or linear chromosomes. In
Escherichia coli, the single circular DNA molecule is
supercoiled - the DNA helix is itself twisted around to form a helix of helical DNA. This supercoiled DNA exists as a
number of loops radiating from a central core. The length and number of loops appears random and changes
dyanmically. The length of individual supercoiled domains (the lengths follow an exponential distribution) averages 10 kb
(kilobases) and their are about 500 such loops or domains per chromosome. Each domain contains DNA that is
negatively supercoiled, meaning that it us unwound or undertwisted slightly (positive supercoiling winds the helix in the
same direction, overwinding it). Supercoiled strands are easier to separate, as must occur during DNA replication and
when the DNA is read by polymerase enzymes to manufacture RNA (see
protein synthesis). It is possibly to demonstrate
supercoiling with a piece of thread or an elastic band - wind it evenly to start with, like a DNA helix, then see what happens
if overwind or underwind it slightly and hold the ends together in a circle. Each domain is separated from neighbouring
domains by an RNA or protein lock. Proteins associated with the nucleoid regulate the amount of supercoiling in each
domain and act to coil/uncoil and bend the DNA to either compact it or unwind it. In this way gene expression can be
regulated - DNA that is too compacted can not be read and is switched off.

In
Bacillus subtilis and Escherichia coli new-born cells have a single chromosome. Most bacteria multiply asexually by
binary fission - a cell grows larger and then splits or divides into two new cells. In elongated cells this division is almost
always occurs perpendicular to the long axis (see bacterial growth). Prior to cell division the single chromosome is
replicated. During replication the double-stranded 'ladder' of the DNA molecule unzips and the exposed single-strands act
as templates against which new single-stranded DNA is synthesised. This  is
semi-conservative replication, meaning
that each new double-stranded daughter chromosome contains one strand from the old parent DNA molecule (the
template strand) and one newly synthesised strand. This is the mode of synthesis found in eukaryotes, such as plants
and animals, too. However, the details of synthesis differ in different organisms. Animals and plants have linear DNA
molecules and synthesis is different from that in the circular DNA of bacteria. In the circular DNA of bacteria, replication
always begins at a specific location on the DNA called the
Ori (origin of replication) and proceeds from the Ori around
the DNA in both directions, ending at another specific location called the
terminus. In the newborn cell the Ori is situated
at one cell pole and the terminus at the opposite cell pole.

During DNA replication, in
Bacillus subtilis and Escherichia coli, the Ori moves to the replisome at the centre/midline of
the cell where division will take place. As DNA synthesis proceeds from the Ori, the daughter Oris move to opposite poles
of the cell, so when division occurs each new daughter cell will have one chromosome with the Ori at one cell pole and the
terminus at the other. More details on DNA replication are given in the section on
bacterial growth. Not all bacteria exhibit
the same pattern, for example in
Caulobacter crescentus swarmer cells, the replisome assembles at the Ori at one cell
pole. As synthesis proceeds the Ori of one daughter chromosome stays put as the other moves to the opposite pole of
the cell and the replisome moves to the centre of the cell as replication proceeds to the terminus. However, the end result
is generally the same - DNA duplicates once per cell cycle so that each daughter cell contains one chromosome with the
Ori at one cell pole and the terminus at the other.
Vibrio cholerae has two chromosomes, one of which replicates in a
similar manner to that of
Caulobacter crescentus, the other has its Ori situated in the centre of the cell.

Chromkinesis, the movement of chromosomes around the cell is well coordinated. Bacteria have a
cytoskeleton that
carries out this function. Although not as complex as the cytoskeleton of a plant or animal cell, the bacterial cytoskeleton
is nevertheless important. Hard to visualise by standard electron microscopy it was a long time before it was realised that
bacteria even have a cytoskeleton. (In animal cells and protoctistans the cytoskeleton is often obvious). At least one
component of the cytoskeleton is responsible for positioning the chromosomes in the cell. The tubular protein MreB forms
spirals along the length of the cell, lying just beneath the inner cell membrane, and is involved in pulling the Oris apart
during replication (and also guides the growth of the peptidoglycan cell wall). The protein FtsK, part of the
divisosome,
also pumps DNA away from the forming cross-wall which will complete division of the cell into two. more details about cell
division are given in the
bacterial growth section.

Many proteins associated with the chromosome in bacteria have functions that are still incompletely understood. These
proteins include HU, IHF and H-NS.

Growth in bacteria

Archaebacteria and extremophiles

Bacterial predators -
Bdellovibrio

Floating around - Prosthecate bacteria

Purple bacteria - a strange twist in the tail

Cyanobacteria - past 'rulers' of the Earth!

Mollicutes (mycoplasmas) - the simplest cells?

Bacterial motility
- learn about one of the smallest known electric motors!

Motility in spirochaetes
- learn about the bacterial inventions of the corkscrew and drill!

Chemokinesis / Chemotaxis
- learn how bacteria use cunning strategies to find their way around.

Bacterial slime cities
-learn about biofilms.

Pili - bacterial appendages with diverse functions
- see more bacterial nanotechnology - bridges, springs and electric wires.

Bacterial sensory systems.

Bacterial communication systems.

Tough materials: the bacterial cell wall.

A strange experiment (updated) - can you solve the mystery of the
anomalous mutations?

Mutants

Coming soon - bacterial power generators.
Bacterial cell structure simplified
Above: a simplified version of the bacterial cell structure diagram, showing the structures most
frequently encountered in elementary biology courses.
Above: another Pov-Ray model of a flagellated bacillus. The bacillus cell-body is essentially a
cylinder with hemispherical end-caps, as modeled here. This version has the flagella
undergoing changes. The flagella of many bacteria have two wavelength modes, one usually
around 1 micrometre wavelength, and the other double this at 2 micrometres - the flagella
can switch between these two modes. They can also flex when they disengage from the
flagellum-bundle as shown here. The flagella have been generated with certain random
parameters, creating a more natural look.

This article last updated: 21/9/2013
Bacterium model
Model bacterium swimming
In these cross-sections, the double membrane, separated by periplasm, characteristic of Gram negative bacteria can be
seen. The outer membrane is budding off
vesicles (a characteristic of Bacteroides fragilis) and the peripheral cytoplasm
is electron-dense (appears dark under the electron microscope) and is rich in ribosomes (dark granules) forming a
riboplasm. Inside the shell of periplasm is the nucleoid, which appears largely transparent (like white spaces, but of
course there are no spaces here in life) with criss-crossing fibrils of DNA. Notice the outer membrane vesicles detaching
from the outside of the cell. This
blebbing is characteristic of Bacteroides fragilis and the vesicles may contain toxins
which are delivered to host cells and so play a role in virulence (
Bacteroides fragilis is a component of the normal
gut-flora in humans, but it can also cause infection, such as intra-abdominal sepsis and bacteremia). In
Pseudomonas
aeruginosa
similar vesicles have been shown to be involved in signalling (they carry quinolone signalling molecules
involved in
quorum sensing).
The diagram above shows a very high magnification image of the cell envelope of Bacteroides fragilis. The double
membrane (outer membrane and inner membrane) are clearly visible. Each membrane displays the trilaminar
(three-layered) appearance characteristic of
unit membrane composed of a double lipid bilayer (two leaflets), with an
electro-lucent (pale layer) sandwiched between two electron-dark layers. Between these membranes is the periplasm,
which contains a thin-layer of peptidoglycan, which some consider to be a gel - certainly it is hard to discern this layer,
though looking at the images above there does seem to be a thin dark layer visible in the middle of the periplasm in some
regions. The outer leaflet of the outer membrane is coated with carbohydrate chains (chains of sugar molecules) called
the
glycocalyx. (In particular the carbohydrate chains of the lipopolysaccharide (LPS) lipid that makes up the outer
leaflet of the OM can be seen here, though additional longer carbohydrate chains are often seen (attached to the LPS)
and these form a slime capsule.

In reality, of course, the bacterial cell is much more complicated, since most of its machinery consists of nanoscale
proteins and other macromolecules which can be seen clearly with standard electron microscopy. The detailed structure
of the ribosome, for example, has been determined by using cryo-electron microscopy, in which the cells are rapidly
frozen (such as with liquid nitrogen) rather than fixed with chemicals, which reduces damage to the cell structure. Very
careful sectioning then allows computer software to reconstruct the 3D structure on a nanometre scale!
A peritrichosuly flagellated bacterium, such as
Escherichia coli and Salmonella. When moving
forward, the flagella come together to form a
propulsive flagella-bundle at the rear of the cell.
Comment on this article!
Thermodiscus has disc-shaped cells only 0.1-0.2 micrometres thick and 0.2 micrometres wide and so has a very small cell
volume.

So, those that obtain nutrients from the water column may have flotation devices, like the prosthecate bacteria. Those
that obtain nutrients from thick mud (or animal skeletons!) may be corkscrew-shaped. Those that obtain nutrients from a
surface may have adhesive structures, such as pili or slime capsules.

Many of these cells are motile - they can swim by means of
flagella (or move in other ways). On this microscopic scale
water behaves as a very viscous treacle-like substance, it has a low Reynold's number, Re (see
biorheology), meaning
that viscosity dominates over inertial forces. The most efficient shape for swimming at such low Re is to have a length
about 3.7 times the width, so rods are more efficient swimmers than spheres. Indeed only about 10% of motile forms are
coccoid. The mean length : width ratio of
Escherichia coli cells (taken over all stages of growth) is about 3.9, very close to
the theoretical optimum. Much longer rods may occur when adhesion is important - a long rod that is aligned parallel to
the direction of fluid-flow has a large surface area with which to adhere to a surface whilst presenting a small area against
the current. When grown in fast-moving currents (high shear forces)
Escherichia coli elongates and may form chains of
cells, a possible adaptation to enhancing adhesion.
Bacillus subtilis responds differently, the cells become smaller and so
present a smaller area to the oncoming fluid. Bacilli dividing by binary fission, tend to adhere to one-another, which
favours the formation of a pavement of cells which covers a surface in such a way as to leave few gaps - the cells are
packed together efficiently.

On the other hand, cocci seem to disperse more easily. There is some evidence that coccoids are carried more easily
through bedrock in underground aquifers, possibly because the rods were adhering to the rock particles more efficiently
along the way. Brownian motion (the jostling of tiny particles due to colliding water molecules) is important in the dispersal
of non-motile forms and is most efficient for spheres, less so for flat cells and least efficient for rods (though there are
other factors involved). Thus, it may be favourable for non-motile forms to be coccoid or to produce coccoid cells for
dispersal (rather like spores).

Finally, it should be realised that bacterial cell shape is not rigid, some bacteria can be rod-shaped or spherical (or some
other shape) depending on the conditions. Most are, however, tiny by cell standards, because they rely on diffusion they
can maximise transport of materials across their cells by being small or at least narrow. Thus, small cocci or long thin cells
are suitable. Bacteria do not have the sophisticated machinery that causes cytoplasm to flow rapidly in plant and animal
cells. This mixing of the cytoplasm and active transport of materials within it allows animal and plant cells to obtain a larger
size.
Internal membranes occur in some bacteria, especially photosynthetic species:
C: cisternae or sacs of membrane – occur as thylakoids in cyanobacteria (the site of photosynthesis);
MI: membrane invaginations - occur in purple bacteria
V: vesicles – occur in a few species

Motor and navigation systems - one or more flagella occur in many bacteria:
FF: flagella filament
FH: flagella hook – a flexible adaptor
FR: flagella rotor – an electric motor whose rotation drives the flagella

GV: gas vacuoles – act as flotation devices and are found in many aquatic species that require light or oxygen
M: magnetosome – found in some bacteria, act as a compass sensitive to the Earth’s magnetic field
Pi: pili – optional appendages that serve multiple functions including adhesion (anchorage), cell docking and
electron transport

Cell envelope - the cell envelope is equipped with various sensors that monitor the environment:
IM: inner membrane – contains generators that convert electrical energy into chemical energy (ATP)
OM: outer membrane – contains lipopolysaccharide (LPS) exotoxin
P: peptidoglycan (in the periplasm) – forms a rigid and very strong cell wall
SC: slime capsule

Synthesis
R: Ribosomes – synthesise proteins, contained in the riboplasm,
PR: polysome, a chain of ribosomes held together by mRNA.
SG: storage granules, store excess sulphur, phosphate, carbohydrate fuels, alcohols and lipids (fats and oils)

Control
N: Nucleoid – contains the chromosome and DNA and DNA-packaging proteins, makes RNA and directs protein
synthesis and hence controls the cell, stores 0.5 to 9.5 Mb of information.
Pd: Plasmid – optional mobile genetic elements that consist of small circles of DNA that can move between
bacteria.
T: tubular proteins - link together to form a cytoskeletal scaffold that directs the movement of enzymes and DNA

N.B. not all bacteria possess all of these structures. Below is a simplified diagram showing those structures most
commonly encountered in a Gram negative bacterium:
model of bacterium
A: Bdellovibrio – a small predatory bacterium which
uses its flagellum to swim at great speeds and gain
entry into other bacteria by ramming them and, if
necessary, digesting a hole through the target cell
wall. Once inside its host bacterial cell it consumes the
host and multiplies before erupting from the dead host.

B: non-motile rods (bacilli, a bacillus is a rod-shaped
bacterium).

C: a chain of photosynthetic and nitrogenfixing
cyanobacteria. Some species are capable of moving
by gliding along surfaces by a largely unknown
mechanism.

D: spherical bacteria (cocci, a coccus is a spherical
bacterium) ensheathed in a slime capsule.

E: a bacillus bearing hairlike spiky appendages called
pili (sing. pilus).

F and G:
prosthecate bacteria containing appendages
called prosthecae (cell extensions) which aid flotation
in water, so these cells can float near the top of seas
and lakes where oxygen is plentiful. F also has gas
vacuoles inside it.

H is a spiral (helical) or corkscrew shaped bacterium.
These bacteria rotate as they swim and so can drill
their way through thick mud, or in the case of the
bacterium that causes syphilis (a
spirochaete) they
can drill through the tissues of the body, including
tough cartilage. They can also eat and damage bones.
bacterial shapes
Transport Processes

The transport of materials affects cell size and shape considerably. Bacteria rely on nutrients reaching the cell, crossing
the cell envelope and then moving around within the cell where they are used. Similarly, toxic wastes must be removed
from the cell. Transport of molecules occurs by two elementary processes: diffusion and convection.
Convection is the
bulk movement of materials in a fluid, such as when hot air rises or when the wind blows or water currents flow
(advection). Convection is a rapid process for moving molecules in bulk. On a smaller scale molecules can also move by
diffusion, which becomes too slow at large scales. An excellent review on bacterial cell shape and size is given by: Young,
Microbiol. Mol. Biol. Rev. 2006, 70(3):660. Some of the key points raised in this review and other articles are summarised
below.

Bacteria vary in diameter from nanobacteria no more than 0.2 micrometres wide, to
Thiomargarita namibiensis, a
colourless sulphur-bacterium 750 micrometres in diameter (much bigger than an average animal cell!) and their mass
varies by 10 orders of magnitude. In large bacteria, inclusions (storage reserves that form granules in the cytoplasm)
reduce the volume of active cytoplasm. Only the fastest and largest swimming bacteria known,
Thiovulum majus, can
increase convective nutrient supply by its own motility, that is it can generate water currents by moving about and these
bacteria actively ventilate their population. Other bacteria are diffusion limited, so can only acquire nutrients that diffuse
to them.

The largest heterotrophic bacterium is the 80 by 600-micrometre large
Epulopiscium spp. This lives in the gut of tropical
fish. This organism possibly exists in a nutrient rich medium. Colourless sulphur bacteria oxidise hydrogen sulphide to
sulphate with oxygen or nitrate. These bacteria form multicellular filaments several cm long, allowing them to penetrate
the 500-micrometre thick diffusive
boundary layer and reach water containing the oxygen or nitrate electron acceptor.
When fluid flows over a solid surface, friction or drag with the surface creates a layer of fluid that is essentially stationary,
this is the boundary layer. Molecules move in and out of the boundary layer predominantly by diffusion rather than by
convection. These bacteria may also store several months reserve of nitrate and sulphur.

Materials moving into and through the bacterium by diffusion must be metabolised by
enzymes. Enzymes are biological
catalysts that speed up the rate of chemical reactions. Each enzyme catalyses one or a few specific reactions and the
molecules that the enzyme acts upon, and changes in some way, are called the
substrate of the enzyme. Without
enzymes, the chemical processes would be too slow to sustain life.
Metabolism is the sum of all the chemical reactions in
the cell. These reactions are of two general types: catabolic reactions break molecules down, whilst anabolic reactions
build molecules up. Thus:
metabolism = catabolism + anabolism.

The
mixing time of small molecules in a one-micrometre bacterium is of the order of one millisecond, that of the larger
molecules 10 milliseconds and enzyme turnover rates are about 100/s (they can metabolise about 100 substrate
molecules per second). Thus, molecules can move through the entire volume of the cell many times during one round of
catalysis (one round of enzyme action). The
traffic time is the theoretical time taken for any two molecules within a cell to
meet. In one second it is probable that any substrate molecule will have met any enzyme molecule. In large prokaryotes,
about 100 micrometres long, the traffic time (which is proportional to the cube of cell length) is about 10 hours. This may
result in regional differences within the cell, or nonbounded compartmentalisation. In other words, this is not a problem
since the cells are narrow, but each section of the cell will be mixing and reacting, but molecules at each end of the cell
will seldom meet and react with one-another.

As well as problems transporting materials within the cell, there are problems in getting nutrients to the cell from outside.
The viscosity of water dampens fluctuations smaller than the
Kolmogorov scale or viscous length, which is about 1 to 6
mm. (This length has its smallest value in the most vigorous turbulence). Cells less than 100 micrometres in diameter are
always surrounded by a
diffusion sphere that is not affected by the surrounding turbulence and hence turbulence is not
locally important for substrate flux to the cell. In other words, they are surrounded by a boundary layer of still water that
does not easily mix with water further from the cell. Substrates must therefore cross this barrier by slow diffusion. Smaller
cell size efficiently relieves the resultant diffusion limitation. Secreting digestive (catabolic) enzymes into the surrounding
water, as many bacteria do, can increase the effective range of substrate utilisation to about 10 micrometres.

The Péclet number is the ratio of transport by convection to transport by diffusion. If Pe >> 1 (>> means: is much greater
than), then fluid flow or swimming strongly enhances the substrate availability. For bacteria, Pe << 1
(<< means is much less than) and so swimming does not increase substrate transport. The minimum size of a cell to
achieve an increase in substrate transport by swimming is about 10 micrometres. Note that we are talking here about
mixing fluid, small bacteria can still obtain more food by swimming towards it, a different process (see
chemokinesis).

Thiovulum majus is an exception. It is a large sulphur-bacteria (about 8 micrometres in diameter, rang from 5 to 25
micrometres, which is very large for a bacterium indeed!). These bacteria increase their substrate uptake 4-fold by
swimming at up to 600 micrometres/s. Their large size and high swimming speed enable them to overcome Brownian
displacement and undergo directional swimming. This is an important point - almost all bacteria capable of motility can
only locate food by altering their turning frequency, a process classically called
chemokinesis, which statistically greatly
increases their likelihood of locating food (see
chemokinesis). They are unable to swim straight to the source of food, a
process called
chemotaxis, because they are too small to discern the direction to the food source (they can not
measure the concentration difference of nutrients detected at each end of the cell). Larger cells, however can do this.
Larger cells can use stereoreceptors to tell them whether or not the chemical 'smells' strongest to the left or right and so
turn straight towards the source. thiovulum is large enough to do just this. It is, as far as i know, unique in bacteria in
carrying out true chemotaxis. [N.B. microbiologists have adopted different definitions of 'chemokinesis' and 'chemotaxis' to
those used here. They call chemokinesis, a change in turning frequency, chemotaxis and refer to changes in speed as
chemotaxis. However, we have used the classical biological definitions whose use we encourage. Chemokinesis can then
refer to a change in velocity, which means speed and/or turning.]

Thiovulum majus is microaerophilic and seeks the oxic-anoxic interface (4% air saturation) ideal for hydrogen sulphide
oxidation. These bacteria maintain their position by U-shaped swimming patterns, they swim and rotate in a helical path (3-
10 rps, r = 5-40 mm, pitch = 40-250 mm). Smaller bacteria must locate optimum conditions by chemokinesis and they do
so by tumbling to change their direction of motion randomly in a bias random walk.

The sediment-water interface

The sediment-water interface has a boundary layer typically of the order of 0.5 mm (500 micrometres). Microbial
respiration in the surface sediment establishes a steep oxygen gradient across this diffusive boundary layer (DBL). The
mean oxygen diffusion time through the DBL is several minutes and there is diffusion limited transport (that is transport
across this layer requires slow diffusion). Filaments or chains of bacterial cells can reach past this boundary layer, to
access nutrients and oxygen. This is one advantage of forming chains of cells. Many cyanobacteria form filaments that
secrete slime sheaths, forming slime tubes. The filaments can glide up and down within this slime tube to access nutrients.

Eukaryotes, such as
ciliates may be stalked (e.g. Vorticella) for the same reason. Zoothamnium niveum is a ciliate that
grows on highly sulphidic mangrove peat. It becomes overgrown by chemoautotrophic, symbiotic sulphur-oxidising
bacteria (hitching a ride to get past the boundary layer). Periodic contractions (every 5-30 s) of its the vorticellid's 15 mm
long stalk generates turbulence (with a Re = 2500) which changes the water adhering to the surface of the symbiotic
bacteria, bringing in fresh nutrients and removing waste.

Big Bacteria (Megabacteria, Gigantobacteria)

Staphylothermus marinus is about 0.5 – 1 micrometres wide, but increases to 15 micrometres in diameter in rich
nutrients. In this enlarged condition, only 2% of the cytoplasm is active, the rest is occupied by a large vacuole. Many
large bacteria are cyanobacteria or sulphide oxidisers.
Thiomargarita namibiensis is about 150 to 200 micrometres wide,
but can be up to 750 micrometres.
Epulopiscium spp. inhabit the guts of herbivorous surgeonfish in the Red Sea and the
Great Barrier Reef and are about 10-20 micrometres wide and 70-200 micrometres long. The large colourless sulphur
bacterium
Achromatium oxaliferum ranges from stores calcium carbonate and sulphur. Big bacteria are found on the sea
floor, where there is a large hydrogen sulphide production and store sulphur for periods of less active volcanic sulphide
venting and can also utilise nitrate as an alternative electron acceptor (see
energy systems). Some grow on mobile
animals, such as
polychaetes, ostracods and mayfly larvae, in sulphide rich environments.

Multicellular Bacteria

Most bacteria form multicellular structures, called biofilms, over solid surfaces at some stage in their life-cycle. The
bacteria communicate with one-another to build these slime structures and in this state they are more resistant to noxious
agents such as antibiotics. Importantly, they can form tower-like structures, about 300 to 400 micrometres long from which
they release swarmer cells, in a spore-like manner, above the stagnant boundary layer where they can be dispersed by
convection. However, although these structures are multicellular, they are not true multicellular organisms, but rather
multicellular societies. In almost all biofilms, the bacteria are never in intimate contact with one-another and do not
communicate directly through special electrical contacts as do cells in a tissue.

Bacterial filaments, chains of cells, can grow up to 7 cm in length. In
magnetotactic forms, there are intercellular
connections (microplasmodesmata) between 10-30 cells for coordination of locomotion. Elecrical currents are thought to
pass between the cells, through these connections, so that they all move in the same direction at the same time.
Connections such as these are the defining feature of true multicellular organisms (animal cells form gap junctions, plant
cells plasmodesmata). Some cyanobacterial filaments have similar connections, as do some other filamentaous bacteria,
including strange forms seen in Antarctica. these filaments are true multicellular organisms, albeit of a simple one-
dimensional type.

Beggiatoa spp. form motile filaments on oxygen - hydrogen sulphide opposed gradients (as hydrogen sulphide
concentration increases, oxygen concentration decreases nearer the sediment surface, the sediments being sulphide
rich) and form dense white mats on marine coasts. These bacteria oxidise hydrogen sulphide with oxygen. They require
both molecules, but can only tolerate low oxygen concentrations, since they are unable to breakdown toxic hydrogen
peroxide that forms at higher oxygen concentrations. These bacteria inhabit the a zone < 1 mm thick at the sediment-
water interface. They consume up to 70% of the sediment’s oxygen and all of its sulphide. Uptake of these molecules is
diffusion limited. The filaments coil-up and are several mm to 1 cm long. The zone of coexisting oxygen and sulphide is
less than 100 mm thick. Thus these bacteria occupy a narrow and specialised niche at the
oxygen/sulphide interface.
These bacteria move by
gliding over solid surfaces and exhibit a phobic response to oxygen concentrations above about
5% air saturation - that is they move away to avoid such 'high' oxygen concentrations. After a 20-30 s delay they reverse
their direction of gliding. When cells at the filament tips encounter oxygen concentrations above the threshold they
retreat, whilst the rest of the filament still glides upwards and as a result the middle part of the filament is forced out to
one side at the oxic-anoxic interface, forming loops. (There would appear to be no coordination of movement along the
filament).

These bacteria also exhibit a phobic response to light. In light the benthic diatoms and
cyanobacteria produce oxygen as
a by-product of photosynthesis, which is toxic to
Beggiatoa. However, at night, organisms continue to respire and use up
oxygen whilst none is made by photosynthesis, and this causes the oxygen – sulphide interface to move above the
sediment. In response to this the filaments move upwards. In the daytime they move downwards. With passing clouds and
changing light levels, the filaments move up and down to track their optimum environment.

Filament gliding movements ensures that the bacteria can break through the diffusiffive barrier or boundary layer, even if
this boundary thickens. When oxygenated water flow decreases filaments move upwards and when oxygenated water flow
decreases the filaments move downwards.

Beggiatoa cells are 5-23 micrometres in diameter and contain sulphur inclusions. This sulphur is oxidised when sulphide
supplies diminish. In eutrophic coastal waters, for example fjords, an anoxic bottom layer of water forms during summer.
This layer may last for days or months. Nitrate can be utilised, instead of oxygen, as an alternative electron acceptor for
sulphide or sulphur oxidation. Nitrate can also penetrate up to 4 cm into the substrate (compared with only several mm for
oxygen). Hydrothermal-vents, hydrocarbon seeps and methane hydrates have high sulphide concentrations and here
form mats of unusually large
Beggiotoa cells (each cell 40-200 micrometres in diameter!) presumably filled with sulphur
reserves. These enlarged cells contain nitrate accumulated in a central vacuole at a concentration up to 160mM. The
mats are > 1 cm thick. Pulsating hydrothermal emissions produces  water flow through the porous spaces in the mats.
This water is cold and oxygen and nitrate rich. The cells stored reserves carry the cells over the periods in-between the
intermittent pulses.

Thiovulum majus is a highly motile, spherical bacterium whose biofilm forms a veil over the sediment surface. The veil may
be attached or partly floating. These bacteria are chemoautotrophs that oxidise hydrogen sulphide to sulphur and
sulphate. Chemoautotrophs can fix their own carbon, but rely on chemical energy to do so rather than light. (Green plants
are photoautotrophs). Each cell is 9-18 micrometres across. The cells are motile, with a maximum speed of 615
micrometres/s (they are the
fastest known bacteria). They swarm to the oxygen – sulphide transition-zone and secrete
a slime thread. The threads stick together and spread-out to form a 2D mesh containing 100 thousand to one million cells
per square centimetre. This mesh separates the flowing oxygenated seawater above from a stagnant boundary layer of
hydrogen sulphide enriched water, hence the veil creates its own diffusive boundary layer suspended in the water
column. This is a truly remarkable phenomenon of 'simple prokaryotes' working together! Concerted swimming actively
moves the veil up or down. The veil may become tethered by slime thread up to 100 micrometres long. The flagella create
a downward water flow of 200 micrometres/s across the veil, which brings in oxygenated water (and possibly sulphide).
The outflows are channeled through numerous small openings in the veil, which has a fine lace appearance. The Péclet
number for oxygen is about 40, in this system, and therefore convection dominates oxygen transport. In this way the cells
collectively acquire more oxygen than they could by diffusion alone.

Commuting

Thioplaca is a marine bacterium with a central vacuole in each cell that can store up to 500 mM nitrate. It forms multicelled
filaments that secrete slime sheaths or tubes around themselves. This organism occurs on shelf sediments and is
sometimes the dominant benthic organism.
Thioplaca only uses nitrate as an electron acceptor. When oxygen
concentrations exceed 10% air saturation, these organisms retreat into their slime sheaths. The winter El Niňo increases
oxygen concentrations in the bottom waters and can reduce the
Thioplaca population dramatically.

Thioplaca secretes slime whilst gliding. This slime forms tubes within which the filaments move along their tracks. Unused
tubes disintegrate rapidly. When up in the water column these bacteria fill their nitrate reservoirs and when down in the
sediment they oxidise sulphide and store sulphur. Thus
Thioplaca has a double storage capacity. In high sulphide
concentrations, the filaments leave their sheaths and live as freely gliding filaments on the sediment surface.

Thiomargarita namibiensis is non-motile and the largest known sulphur bacterium. It inhabits semi-fluid diatom ooze where
sulphide concentrations are greater than 10 mM. These cells only contact nitrate and oxygen when the loose sediment is
suspended in the water column following storms, wave pumping or methane eruptions. They have a vacuole occupying
98% of the cell volume. They can respire for 40-50 days or more without taking up new nitrate (for over two years in a
cold room). They can survive in air-saturated water and can use oxygen as an electron-acceptor for sulphide oxidation.

Internal structure

Although not as complex as animal or plant cells, bacteria still contain machinery consisting of thousands of
working parts
, but you need to zoom in to the nanometre scale (one nanometre, 1 nm, is one millionth of a millimetre)
to see this complex machinery!

Let's take a slightly closer look at a section through a bacterium (click to enlarge):
Left: Vibrio is a comma-shaped bacterium, similar in contour
to
Bdellovibrio. Comma-shaped bacteria are similar to the
helical spirochaetes except that instead of spanning many
turns of the helix they have less than a single turn along their
length. This shape probably aids locomotion to some extent
in slightly viscous media. Some species of
Vibrio may have
mixed flagellation: lots of flagella around the surface of the
cell (
peritrichous flagellation) and a thicker flagellum at one
cell pole. In liquid culture
Vibrio has a single sheathed
flagellum at one pole of the cell (a sheathed flagellum is a
normal bacterial flagellum covered by the outer membrane,
more commonly, bacterial flagella have no membranous
sheath. However, when grown on solid agar it develops
additional unsheathed flagella that give it the motive power to
crawl over the agar in a phenomenon called
swarming.
Vibrio
Gram negative bacterial cell - unlabeled
Gram positive bacterial cell
Gram positive bacterial cell - unlabeled
Gram negative bacterial cell
Above: the structure of a Gram negative bacterial cell.
Left: an unlabeled version for your own
use.

Right: the structure of a Gram positive
bacterial cell, labeled and unlabeled.