
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.

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.

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.
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.


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





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.
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:


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.

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.
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.