Purple Bacteria
The purple bacteria are one of the groups of photosynthetic bacteria (the other main groups being the cyanobacteria
and green bacteria, though halobacterium can use light as an energy source it is not photosynthetic). They fall into
two groups, according to their metabolism (each group appears to be an assembly of different lineages that evolved
separately):
purple non-sulphur bacteria (e.g. Rhodospirillum, Rhodobacter) and purple sulphur bacteria.
Purple sulphur bacteria can use elemental sulphur and also sulphide (e.g. hydrogen sulphide) as an electron-donor in
respiration, whilst non-sulphur bacteria can not, but use an organic electron-donor instead (e.g. succinate, malate) or
elemental hydrogen.

Purple sulphur and purple non-sulphur bacteria and an overview of bacterial energy metabolism

Bacterial metabolism is a very complex topic, because bacteria are very metabolically diverse. The purple bacteria are
good examples to illustrate many of the features.

Recall that
respiration is a complex redox (reduction-oxidation) reaction (consisting of a chain of smaller redox
reactions) in which fuel (the
initial electron donor) is oxidised to release energy, that is the fuel loses one or more
electrons, which carry the energy, by passing them onto the first link in an electron transport chain (ETC, a chain of
specific biochemicals) which gains the electron and so becomes reduced (OIL RIG: oxidation is loss of electrons,
reduction is gain). The electron is then passed sequentially from link-to-link down the chain, as components of the
chain become alternately oxidised and reduced whilst the electron loses energy at each step (this flow of electrons is
essentially the flow of electric charge or electricity). Much of the energy lost by the electron is harvested and
converted into chemical energy where it is stored until needed, usually in molecules of ATP. (Initially the energy is
used to pump protons across the (inner) cell membrane and these protons then flow through the ATPase molecular
motors, causing them to rotate and this rotaional mechanical energy is converted into chemical energy in ATP). The
electron finally exits the ETC, having lost much of its energy, and reduces the
final electron-acceptor, which in
animal cells is oxygen which become reduced to water. Bacteria are metabolically very diverse and some make use of
other electron acceptors (reducible substances), according to what is most readily available in their habitat. Similarly
they can use a variety of initial electron donors (oxidisable substances or fuels).

Photosynthesis is also a redox chain which harnesses light energy to build complex organic molecules (including fuels
for respiration) from simple carbon compounds, including carbon dioxide (as in plants) or simple water-soluble organic
carbon sources like acetate and other organic acids. Photosynthesis must always be accompanied by respiration - it is
an addition not an alternative, it simply uses light energy to generate the carbon fuels for respiration (such as sugars
like maltose and glucose) and other organic building blocks (like amino acids, lipids and nucleotides). Light oxidises
the light-receptive pigments (chlorophylls and carotenoids in plants, bacteriochlorophyll in bacteria) which pass an
electron through an ETC. The electron loses energy as it passes down the ETC and this energy is used to build
organic molecules from the simpler carbon sources (like carbon dioxide or acetate). In non-cyclic systems, the electron
must arrive at a final electron-acceptor (NADP in plants). In cyclic systems, there is no net oxidation or reduction,
rather electrons are channeled through a circuit. An
electron donor is needed to replace the electron lost by the
chlorophyll in plants and this is water which is split by plants, generating oxygen. We shall look at the system in purple
bacteria in more detail in the 'Photosynthesis' section below.

The terms used in describing the energy metabolism of organisms can be very confusing at first, so lets look at a few
more key terms:

Heterotrophs are organisms, like animals, which obtain their carbon by breaking-down organic molecules built by
other organisms. The term usually refers to
chemoheterotrophs, like animals, who use these ready-made carbon-
sources also as fuels, to supply energy by respiration. However some bacteria are
phototoheterotrophs, using light
as a source of energy (rather than chemical fuel) but ready-made organic sources for a supply of carbon.

Autotrophs make their own organic molecules from simple carbon molecules readily available in the environment
such as carbon dioxide from the air (we can think of these materials as readily available abiotically, though in reality
natural cycles involving living organisms are needed to maintain supplies). In the case of utilising a gas, like carbon
dioxide, and using it to make 'solid' materials like proteins, we say that the carbon has been
fixed (made 'solid'). We
usually think of plants which are
photoautotrophs, using light as an energy source and carbon dioxide as a carbon
source to build their own materials by photosynthesis. However, some bacteria are
chemoautotrophs, using
chemical fuels as a source of energy to synthesise their own materials from simple carbon sources.

Chemotrophs is a generic term referring to organisms that use chemical reactions as their chief source of energy,
that is chemoheterotrophs and chemoautotrophs collectively. (Lit. 'chemical-eating').

Phototrophs similar refers to photoautotrophs and photoheterotrophs - organisms that use light as thei chief source
of energy. (Lit. 'light-eating').

  • Purple bacteria can grow photoautotrophically (photosynthetically using light to fix a simple inorganic carbon
    source) in anaerobic conditions (in the absence of air) using carbon dioxide as the carbon-source and
    hydrogen as the electron donor.

  • They can also grow photoheterotrophically (photosynthetically using light and an organic carbon source)
    under anaerobic conditions, on such organic carbon sources as acetate, malate and succinate (salts of organic
    acids) which act as electron donors.

  • Some can also grow as chemoheterotrophs (heterotrophs, by respiring organic fuels / carbon sources) in the
    dark, under aerobic conditions (using oxygen as the final electron acceptor). [Some non-sulphur types only].

Photosynthesis

In bacteria, as in plants, antenna pigments trap light energy and then pass this on to light-sensitive pigments in the
reaction centres (which may also catch light directly, but the antenna pigments greatly enhance the efficiency of
photon capture). Purple bacteria contain bacteriochlorophyll type a or b as the primary light-sensitive pigment in the
reaction centres and antennae, and in the antenna carotenoids enhance the range of wavelengths of light that can be
harnessed. These carotenoids may be purple, red, brown or orange in colour and give the bacteria their characteristic
colouration.

Purple bacteria are Gram negatives and so possess a double membrane in the cell envelope. The inner membrane is
extensively folded into sacs, tubes or sheets, increasing its surface area, and most of the photosynthetic machinery is
located on these folds. These folds contain 3 types of molecular complexes involved in photosynthesis:

1) Antenna or
light-harvesting complexes (LHC);
2)
Reaction centres (RC);
3)
Cytochrome (cyt) bc1 complex.

A
biomolecular complex is a close association of biochemicals into a working unit, which minimises the distances
reactants must diffuse in order to react to one-another and greatly increases efficiency (a ribosome is another
example of a biomolecular complex). The antenna or LHC binds carotenoids and bacteriochlorophyll (bchl) molecules
and collects incident light. In most purple bacteria, including
Rhodobacter sphaeroides, there are two types: LHC1 and
LHC2. The amount of LHC2 is variable and dependent on environmental conditions, such as the amount of oxygen
present and light intensity. The ratio of LHC1 to RC is fixed as these combine to form a RC-LHC1 supercomplex. There
are as many as 100 bacteriochlorophyll molecules in each RC, increasing the amount of incident light that can be
absorbed. At the core of each RC is a
bchl-dimer (bacteriochlorophyll dimer, two bchl molecules joined together).

Photosynthesis in these organisms is cyclic, and does not produce oxygen. The sequence of events, as worked-out
for
Rhodobacter sphaeroides, is as follows:

  1. A photon is absorbed by the LHC, causing it to lose an electron to the RC in less than 100 ps (ps =
    picosecond). If absorbed by LHC2 then the electron is passed to LHC1.
  2. The electron is passed to bchl in the RC and on to the core bchl-dimer in the RC which acts as the primary
    electron donor for the ETC and passes an electron to bacteriophytin in 2-3 ps.
  3. Bacteriophytin passes an electron to the next link in the cycle, a quinone molecule (QA) in about 200 ps.
  4. the electron is passed on to a second quinone (QB).
  5. Steps 1-4 are repeated until QB is carrying two electrons.
  6. The reduced QB picks up two protons from the cytosol, forming QBH2 (quinol).
  7. The quinol is released from the RC and delivers its two protons to the periplasm (the region between the inner
    and outer cell membranes), a reaction mediated by the Rieske protein (which contains catalytic Fe2S2 iron
    sulphide clusters) and the cyt bc1 complex. The electrons are passed on to cytochrome c2 (cyt c2).
  8. Cyt c2 completes the cycle by passing the electrons back to bacteriochlorophyll, replacing the electrons lost
    initially.

The tremendous speed with which the electron is initially transferred from the LHC to the RC ensures very efficient
electron capture. The quantum yield (ratio of electrons produced per photon absorbed) is almost 1. (There is always a
possibility that a molecule will absorb a photon and de-excite by some other means, with the energy wasted. This can
never be eliminated, but it can be minimised).

Under certain conditions,
Rhodobacter sphaeroides produces membrane invaginations free of LHC2, this simplified
membrane-system has been studied in great structural detail and it is found to be studded in complexes as shown
below:
Above: Rhodobacter spheroides with its single flagellum inserted in the side
of the cell.
Left: the membrane supercomplexes of Rhodobacter each
repeating unit is 19.8 by 11.2 nanometres. In vitro, two rings of
LHC1 form around the RC, however, in vivo, each ring is open,
resulting in an S-shaped supercomplex, likely due to LHC1. The
regions inside each incomplete ring of the S-upercomplex
(shown stipled) is likely to be a RC. The small detached
structure between adjacent S-supercomplexes could be the
cytochrome bc1 complex and then quinones would have only a
short distance to diffuse bewteen the RC and the cyt bc1
(diffusing through the gaps in the S-shaped rings).

The protein PufX is needed for the formation of S-shaped
dimers, as opposed to closed rings, and this protein may thus
function to prevent formation of a closed ring, allowing
quinones to diffuse to the cyt bc1 and back.

The grouping of the photosystem into these highly organised
membrane complexes and supercomplexes sppeds up the
reaction, since diffusion is kept to a minimum. Indeed, the
system still functions in membranes frozen at -20 C, illustrated
how the system is not diffusion limited. This is an excellent
example of how the nanomachinery of cells can be highly
organised, something which becomes ever increasingly
apparent with ongoing research. The old model of a cell as a
'bag of chemicals' is far from the truth.
Locomotion and Chemokinesis/Chemotaxis

Rhodobacter sphaeroides demonstrates an interesting variation on bacterial locomotion, which is quite different from
the run and tumble behaviour of peritrichously flagellated
Escherichia coli. Rhodobacter will undergo chemokinesis
(often referred to as chemotaxis, erroneously in my opinion, though these terms are not very self-describing and can
be misleading - see the article on
chemokinesis for the definitions we have adopted, which agree with standard biology
textbook definitions) towards nutrients, that is positive chemokinesis. This is a form of
klinokinesis. In klinokinesis
changes in turning frequency occur in response to changes in stimulus strength. Turning frequency changes in
response to
temporal changes in stimulant concentration. As in Escherichia coli, the cells swim about and so compare
stimulus strengths at different spatial positions
at different times. They have a cellular memory (the response
habituates) and so are able to detect a drop or increase in stimulant concentration as they move about and hence
indirectly detect chemical gradients. This is NOT chemotaxis, as defined in ethology, in which the gradient is measured
directly in one instant of time at each spatial position, for example by having widely spaced sensors to give a stereo
view of the odour gradient. Only the very largest bacteria exhibit true chemotaxis, most are simply too small to measure
spatial gradients directly.
Having only one flagellum necessitates a different
mechanism of cell turning than the random tumbling of
Escherichia coli. Some bacteria with a single polar
flagellum alternate the direction of flagellum rotation,
causing it to push or pull. Similarly, bacteria with one or
more flagella at each pole can switch each bundle from
pushing to pulling (see
Halobacterium for example).
However, the flagellum of
Rhodobacter does not change
direction, it can only rotate clockwise (or
counterclockwise ion some strains) and is a right-handed
helix. However, it can coil-up close to the cell body (by
reducing wavelength and increasing amplitude, the
switch occuring from the tip towards the base) and rotate
slowly. This slowly rotating coil turns the cell (in
conjunction with Brownian motion) and is functionally
similar to the tumbles exhibited by
Escherichia coli. This
is the mode of chemokinesis demonstrated under
anaerobic conditions. Positive chemokinesis in response
to nutrients has been observed.
The response of Rhodobacter is pessimistic: it increases turning frequency as it moves down an attractant gradient.
This is in contrast to the
optimistic response shown by Escherichia coli in which tumbling frequency reduces as it
moves up an attractant gradient.
Rhodobacter swims at about 35 micrometres per second (compared to 20-30
micrometres per second for
Escherichia coli).

In aerobic conditions, the behaviour becomes more complicated and changes in flagella rotation speed can also cause
the cell to turn in an arc when the rotation rate slows. A change in speed of locomotion in response to a change in
strength of a stimulus is
orthokinesis (though in microbiology literature this is usually erroneously defined exclusively
as chemokinesis, but chemokinesis can involve changes in turning frequency and/or speed of locomotion - the terms
'kinesis' and 'kinetic' refer to motion or velocity, that is speed AND direction, so BOTH orthokinesis and klinokinesis are
types of kinesis).
The diagram above shows the distribution of bacteria in a typical freshwater lake in which the water is stratified. The
thermocline is the depth at which the temperature suddenly changes and defines the epilimnion above and the
hypolimnion below. In the epilmnion, photosynthetic bacteria, such as the cyanobacteria, may contribute significantly to
primary productivity (the fixation of carbon dioxide into organic carbon, in this case by photosynthesis requiring light).
(Eukaryotic algae usually make the larger contribution). If the lake is more-or-less stagnant, then the sediments will be
anoxic (lacking in oxygen) and anaerobic bacteria will dominate here. These bacteria may be strict anaerobes, that can
only grow in the absence of oxygen (like
Clostridium) or organisms that can grow anaerobically when they need to (like
Pseudomonas). Heterotrophs are those bacteria that break-down organic materials as a fuel and carbon-source.
These are most abundant in the thermocline (aerobes) and in the sediments (anaerobes) or wherever organic material
is most abundant. Sulphate may be injected into the lake in sea water or sulphate-rich springs.

The products of anaerobic decomposition of these organic materials (e.g. the remains of dead organisms) include
methane gas (CH4), ammonia gas (NH3) which dissolves to give ammonium (NH4+) and hydrogen sulphide gas (H2S).
Hydrogen sulphide gas is toxic and if too much is produced, as it can be in stagnant waters with excess organic
materials, then fish and other organisms may die. It is fortunate. Therefore, that higher in the water column there are
the green and purple sulphur bacteria which can utilise this hydrogen sulphide and convert it into elemental sulphur.
These bacteria require some light and so occur near the surface, below the cyanobacteria, where there is still sufficient
light, but where their sulphide source can be found. These organisms keep the upper oxygenated waters largely free
of hydrogen sulphide in a healthy lake.

Purple sulphur bacteria

E.g. Thiospirillum, Ectothiorhodospira, Chromatium, Thiocystis, Thiocapsa, Lamprocystis, Thiodictyon, Thiopedia,
Amoebobacter
. These are strictly anaerobic and grow predominantly photoautotrophically (using light to fix carbon and
hydrogen as the electron donor). They use
hydrogen sulphide as an electron donor (oxidising it to sulphur and then
more slowly to sulphate) and assimilate carbon dioxide (largely through the Calvin-Benson cycle) and produce their
ATP by cyclic photophosphorylation.
Purple sulphur bacteria are obligate phototrophs, and require light in order to grow.

Purple Non-sulphur Bacteria

E.g. Rhodospirillum, Rhodopseudomonas, Rhodomicrobium, Rhodopila, Rhodocyclus, Rhodobacter.

These are predominantly anaerobic photoheterotrophic using fatty acids, other organic acids, primary and secondary
alcohols, carbohydrates and aromatic organic compounds as their carbon source. They can also respire these
compounds in the dark (
chemoheterotrophism).

They are sensitive to hydrogen sulphide, which inhibits their growth, although some can oxidise very low levels of
sulphide anaerobically in the light. They typically occur in freshwater lakes and ponds where organic matter is present
but sulphide is low.

Rhodobacter capsulatus is able to grow as an aerobic chemoautotroph (assimilating carbon but by using chemical
energy rather than light) in the dark with hydrogen as the electron donor. Contrast this with purple sulphur bacteria
which are obligate phototrophs.

Denitrification

Some purple non-sulphur bacteria, e.g. Rhodopseudomonas palustris and Rhodobacter sphaeroides, can denitrify,
that is reduce nitrate (which is reduced to nitrite then to nitrogen, with each denitrifying bacterium capable of one or
both stages) by respiring it anaerobically instead of oxygen when oxygen is exhausted.
Purple sulphur bacteria can also grow photoheterotrophically, that is using light and an organic carbon source.