5
Bacteria and Marine Biogeochemistry
188
5.4.7
Respiration and Fermentation
The best known type of energy metabolism in the
seabed is the aerobic respiration by heterotrophic
organisms such as animals and many bacteria.
Heterotrophic bacteria take up small organic
molecules such as glucose, break them down into
smaller units, and ultimately oxidize them to CO 2
with oxygen. The first pathway inside the cell,
called glycolysis, converts glucose to pyruvate
and conserves only a small amount of potential
energy in ATP (Fig. 5.10). Only few electrons are
transferred to NAD
+
to form reduced NADH.
Through the complex cyclic pathway called the
tricarboxylic acid cycle (TCA cycle), the rest of
the available electrons of the organic substrate is
transferred, again mostly to form NADH, and CO 2
is released. The electron carrier, NADH, is
recycled by transferring its electrons via a
membrane-bound electron transport chain to the
terminal electron acceptor, O 2 , which is thereby
reduced to H 2 O. Through the electron transport
chain, the proton-motive force across the cell
membrane is maintained and most of the energy
carrier, ATP, is generated. The energy yield of
aerobic respiration is large, and up to 38 mol of
ATP may be formed per mol of glucose oxidized.
This corresponds to a 43% efficiency of energy
utilization of the organic substrate, the rest being
lost as entropy (heat). By the transfer of electrons
from the electron carrier, NADH, to the terminal
electron acceptor, O 2 , the reduced form of the
carrier, NAD
+
, is regenerated and the electron flow
can proceed in a cyclic manner.
Many heterotrophic prokaryotes are anaerobic
and have the ability to use terminal electron
acceptors other than O 2 for the oxidation of their
organic substrates (Fig. 5.10). The denitrifying
bacteria respire with NO 3
-
which they reduce to N 2
and release into the large atmospheric nitrogen
pool. The sulfate reducing bacteria can use a
range of organic molecules as substrates and
oxidize these with the concomitant reduction of
SO 4
2to H 2 S. Some bacteria can use manganese(III, IV) or iron(III) oxides as electron
acceptors in their heterotrophic metabolism and
reduce these to Mn
2+
or Fe
2+
.
Many bacteria do not possess a complete
TCA-cycle and electron transport chain and are
thus not able to use an external electron acceptor
as terminal oxidant. This prevents the formation of
large amounts of ATP via the electron transport
chain and thus leads to a low energy yield of the
metabolism. The organisms may still form a small
amount of ATP by so-called substrate level
phosphorylation through the glycolysis, and this
is sufficient to enable growth of these fermentative organisms. The cells must, however, still be
able to recycle the reduced electron carrier,
NADH, in order to continue the glycolytic
pathway. In principle, they do this by transferring
the electrons from NADH to an intermediate such
as pyruvate (CH 3 COCOO
–
). An example of a
fermentation reaction is the formation of lactate
(CH 3 CHOHCOO
–
) by lactic acid bacteria (brackets
around the pyruvate indicate that this is an
intermediate and not an external substrate being
assimilated and transformed):
[CH 3 COCOO - ] + NADH + H + →
CH 3 CHOHCOO - + NAD +
(5.24)
It is seen that fermentation does not require an
external electron acceptor and there is no net
oxidation of the organic substrate, glucose. There
is rather a reallocation of electrons and hydrogen
atoms within the cleaved molecule, whereby a
small amount of energy is released. Fermentations
often involve a cleavage of the C 3 compound to a
C 2 compound plus CO 2 . The pyruvate is then
coupled to coenzyme-A and cleaved in the form of
acetyl-CoA and energy is subsequently conserved by the release of acetate (CH 3 COO
–
):
[CH 3 COCOO - ] → CH 3 COO - + CO 2 + H 2
(5.25)
The H 2 is formed by a transfer of electrons from
pyruvate via the enzyme ferredoxin to NAD + :
NADH + H + → NAD + + H 2
(5.26)
The degradation of organic matter via fermentative pathways to small organic molecules such
as lactate, butyrate, propionate, acetate, formate,
H 2 and CO 2 is very important in marine sediments,
since these compounds are the main substrates
for sulfate reduction and partly for methane
formation.
A form of inorganic fermentation of sulfur
compounds was discovered in recent years in
several sulfate reducers and other anaerobic
bacteria (Bak and Cypionka 1987). These
organisms may carry out a disproportionation of
S
0
, S 2 O 3
2or SO 3
2by which H 2 S and SO 4
2are
formed simultaneously (Eqs. 5.4 and 5.5).
Disproportionation reactions have turned out to
Bacteria and Marine Biogeochemistry
188
5.4.7
Respiration and Fermentation
The best known type of energy metabolism in the
seabed is the aerobic respiration by heterotrophic
organisms such as animals and many bacteria.
Heterotrophic bacteria take up small organic
molecules such as glucose, break them down into
smaller units, and ultimately oxidize them to CO 2
with oxygen. The first pathway inside the cell,
called glycolysis, converts glucose to pyruvate
and conserves only a small amount of potential
energy in ATP (Fig. 5.10). Only few electrons are
transferred to NAD
+
to form reduced NADH.
Through the complex cyclic pathway called the
tricarboxylic acid cycle (TCA cycle), the rest of
the available electrons of the organic substrate is
transferred, again mostly to form NADH, and CO 2
is released. The electron carrier, NADH, is
recycled by transferring its electrons via a
membrane-bound electron transport chain to the
terminal electron acceptor, O 2 , which is thereby
reduced to H 2 O. Through the electron transport
chain, the proton-motive force across the cell
membrane is maintained and most of the energy
carrier, ATP, is generated. The energy yield of
aerobic respiration is large, and up to 38 mol of
ATP may be formed per mol of glucose oxidized.
This corresponds to a 43% efficiency of energy
utilization of the organic substrate, the rest being
lost as entropy (heat). By the transfer of electrons
from the electron carrier, NADH, to the terminal
electron acceptor, O 2 , the reduced form of the
carrier, NAD
+
, is regenerated and the electron flow
can proceed in a cyclic manner.
Many heterotrophic prokaryotes are anaerobic
and have the ability to use terminal electron
acceptors other than O 2 for the oxidation of their
organic substrates (Fig. 5.10). The denitrifying
bacteria respire with NO 3
-
which they reduce to N 2
and release into the large atmospheric nitrogen
pool. The sulfate reducing bacteria can use a
range of organic molecules as substrates and
oxidize these with the concomitant reduction of
SO 4
2to H 2 S. Some bacteria can use manganese(III, IV) or iron(III) oxides as electron
acceptors in their heterotrophic metabolism and
reduce these to Mn
2+
or Fe
2+
.
Many bacteria do not possess a complete
TCA-cycle and electron transport chain and are
thus not able to use an external electron acceptor
as terminal oxidant. This prevents the formation of
large amounts of ATP via the electron transport
chain and thus leads to a low energy yield of the
metabolism. The organisms may still form a small
amount of ATP by so-called substrate level
phosphorylation through the glycolysis, and this
is sufficient to enable growth of these fermentative organisms. The cells must, however, still be
able to recycle the reduced electron carrier,
NADH, in order to continue the glycolytic
pathway. In principle, they do this by transferring
the electrons from NADH to an intermediate such
as pyruvate (CH 3 COCOO
–
). An example of a
fermentation reaction is the formation of lactate
(CH 3 CHOHCOO
–
) by lactic acid bacteria (brackets
around the pyruvate indicate that this is an
intermediate and not an external substrate being
assimilated and transformed):
[CH 3 COCOO - ] + NADH + H + →
CH 3 CHOHCOO - + NAD +
(5.24)
It is seen that fermentation does not require an
external electron acceptor and there is no net
oxidation of the organic substrate, glucose. There
is rather a reallocation of electrons and hydrogen
atoms within the cleaved molecule, whereby a
small amount of energy is released. Fermentations
often involve a cleavage of the C 3 compound to a
C 2 compound plus CO 2 . The pyruvate is then
coupled to coenzyme-A and cleaved in the form of
acetyl-CoA and energy is subsequently conserved by the release of acetate (CH 3 COO
–
):
[CH 3 COCOO - ] → CH 3 COO - + CO 2 + H 2
(5.25)
The H 2 is formed by a transfer of electrons from
pyruvate via the enzyme ferredoxin to NAD + :
NADH + H + → NAD + + H 2
(5.26)
The degradation of organic matter via fermentative pathways to small organic molecules such
as lactate, butyrate, propionate, acetate, formate,
H 2 and CO 2 is very important in marine sediments,
since these compounds are the main substrates
for sulfate reduction and partly for methane
formation.
A form of inorganic fermentation of sulfur
compounds was discovered in recent years in
several sulfate reducers and other anaerobic
bacteria (Bak and Cypionka 1987). These
organisms may carry out a disproportionation of
S
0
, S 2 O 3
2or SO 3
2by which H 2 S and SO 4
2are
formed simultaneously (Eqs. 5.4 and 5.5).
Disproportionation reactions have turned out to