HC12 Metabolic diversity III –
Nitrogen and sulphur cycle
(BOOK)
Chapter 14.6, 14.9 and 14.11-14.13
CH14 Metabolic Diversity of Microorganisms
14.6 Nitrogen Fixation
The formation of ammonia from gaseous dinitrogen (N2) is called nitrogen fixation. Only certain
species of bacteria and archaea can fix nitrogen.
Nitrogen fixation is catalysed by an enzyme complex called nitrogenase which consists of two
proteins that both contain iron:
- Dinitrogenase
- Dinitrogenase reductase contains molybdenum as well and is
part of the iron-molybdenum cofactor (FeMo-co) and this is
the site where N2 reduction occurs.
Nitrogen fixation is inhibited by oxygen because dinitrogenase
reductase is irreversibly inactivated by O2.
In heterocystous cyanobacteria, nitrogenase is protected by the cell
in which it is located called an heterocyst which shuts down oxygen
production inside.
Due to the triple bond in N2, the activation and reduction is very
energy demanding. Six electrons are necessary to reduce N2 to two
NH3 but eight electrons are consumed because two are lost as H2 for
each mole of N2 reduced. In addition to electrons, ATP is required
and lowers the reduction potential of dinitrogenase reductase.
14.9 Oxidation of Sulfur Compounds
The most common sulfur compounds used as electron donors are hydrogen sulfide (H2S) elemental
sulfur (S0) and thiosulfate (S2O32-). However in most cases the final oxidation product is sulfate (SO 42-).
There are diverse pathways for conserving energy from the oxidation of sulfur compounds. One is
the sox system. There are four key proteins in the sox system, all present in the periplasm:
- SoxXA
- SoxYZ
- SoxB
- SoxCD
It begins when SoxXA forms a heterodisulfide bond between the sulfur compound to be oxidised and
the carrier protein, SoxYZ. The sulfur compound remains bound to the carrier throughout the
pathway and being ultimately released by SoxB. SoxCD mediates the removal of 6 electrons from the
sulfur compound bound to the carrier. Electrons from the system are funnelled into the ETC while
protons are released to acidify the external environment.
Some sulfur-oxidising microbes that store sulfur granules also use components of the Sox system but
lack the key enzyme SoxCD which means that the sulfur atom bound to SoxYZ is added to a growing
, sulfur granule in the periplasm. The sulfur in the granule can be reductively activated and
transported to the cytoplasm where it is eventually oxidised to sulfite (SO 32-) by the reverse activity of
DsrAB.
Sulfite reducties can then oxidise sulfite and transfer the electrons to the ETC.
14.10 Iron (Fe2+) oxidation
The aerobic oxidation of ferrous iron (Fe2+) to ferric iron (Fe3+) supports growth of
chemolithotrophic iron bacteria. However, at acidic pH only a small amount of energy is available
from this reaction.
Because the reduction potential of the Fe2+/Fe3+ couple is so high, steps in electron transport to
oxygen can obviously be few. Iron oxidation begins in the outer membrane where the organism
contacts ferrous iron which is than oxidised to ferric iron which is a one electron transition. This
reaction is thought to be pulled forward by the consumption of ferric iron in Fe(OH)3 formation.
The nature of the proton motive force in highly acidic environments is interesting because a large
gradient of protons already exists across the cytoplasmic membrane. However, the organism cannot
make ATP from this preformed proton motive force in the absence of an electron donor. This is
because H+ ions that enter the cytoplasm via ATPase must be consumed in order to maintain the
internal pH within acceptable limits.
Autotrophy is supported by the Calvin cycle and because the high potential of the electron donor,
much energy must be consumed in revere electron flow reactions to obtain the reducing power
(NADH) to drive the CO2 fixation.
Ferrous iron can also be oxidised under anoxic conditions in which Fe2+ is used either as an electron
donor in energy metabolism and/or as a reductant for CO2 fixation.
14.11 Nitrification
Nitrification is the process in which nitrifying bacteria oxidise ammonia and nitrite. Nitrification
consists of two different sets of reactions:
1. Catalyse oxidation of ammonia to nitrite
2. Catalyse oxidation of nitrite to nitrate
Most nitrifying microbes are only capable of catalysing one of the two reactions mentioned above.
The bioenergetics of nitrification is based on the same principles that govern other
chemolithotrophic reactions: electrons from reduced inorganic substrates enter an ETC and electron
transport reactions establish a pmf that drives ATP synthesis. The complete oxidation of NH3 to NO3-
involves an eight electron transfer and the electron donors for the nitrifying bacteria are not
particularly strong.
NH3 is oxidised to NH2OH by ammonia monooxygenase (ammonia oxidising bacteria)
NH2OH is oxidised to NO2- by hydroxylamine oxidoreductase (ammonia oxidising bacteria)
NO2- is oxidised to NO3- by nitrite oxidoreductase (nitrite oxidising bacteria)
Like sulfur- and iron-oxidising chemolithotrophs, aerobic nitrifying bacteria employ the Calvin cycle
for CO2 fixation.
Recall that CO2 fixation is the process by which inorganic carbon is converted to organic compounds.
14.12 Anaerobic Ammonia Oxidation (Anammox)
NH3 can also be oxidised under anaerobic conditions, this process is called anammox.
The anammox reaction is;
Nitrogen and sulphur cycle
(BOOK)
Chapter 14.6, 14.9 and 14.11-14.13
CH14 Metabolic Diversity of Microorganisms
14.6 Nitrogen Fixation
The formation of ammonia from gaseous dinitrogen (N2) is called nitrogen fixation. Only certain
species of bacteria and archaea can fix nitrogen.
Nitrogen fixation is catalysed by an enzyme complex called nitrogenase which consists of two
proteins that both contain iron:
- Dinitrogenase
- Dinitrogenase reductase contains molybdenum as well and is
part of the iron-molybdenum cofactor (FeMo-co) and this is
the site where N2 reduction occurs.
Nitrogen fixation is inhibited by oxygen because dinitrogenase
reductase is irreversibly inactivated by O2.
In heterocystous cyanobacteria, nitrogenase is protected by the cell
in which it is located called an heterocyst which shuts down oxygen
production inside.
Due to the triple bond in N2, the activation and reduction is very
energy demanding. Six electrons are necessary to reduce N2 to two
NH3 but eight electrons are consumed because two are lost as H2 for
each mole of N2 reduced. In addition to electrons, ATP is required
and lowers the reduction potential of dinitrogenase reductase.
14.9 Oxidation of Sulfur Compounds
The most common sulfur compounds used as electron donors are hydrogen sulfide (H2S) elemental
sulfur (S0) and thiosulfate (S2O32-). However in most cases the final oxidation product is sulfate (SO 42-).
There are diverse pathways for conserving energy from the oxidation of sulfur compounds. One is
the sox system. There are four key proteins in the sox system, all present in the periplasm:
- SoxXA
- SoxYZ
- SoxB
- SoxCD
It begins when SoxXA forms a heterodisulfide bond between the sulfur compound to be oxidised and
the carrier protein, SoxYZ. The sulfur compound remains bound to the carrier throughout the
pathway and being ultimately released by SoxB. SoxCD mediates the removal of 6 electrons from the
sulfur compound bound to the carrier. Electrons from the system are funnelled into the ETC while
protons are released to acidify the external environment.
Some sulfur-oxidising microbes that store sulfur granules also use components of the Sox system but
lack the key enzyme SoxCD which means that the sulfur atom bound to SoxYZ is added to a growing
, sulfur granule in the periplasm. The sulfur in the granule can be reductively activated and
transported to the cytoplasm where it is eventually oxidised to sulfite (SO 32-) by the reverse activity of
DsrAB.
Sulfite reducties can then oxidise sulfite and transfer the electrons to the ETC.
14.10 Iron (Fe2+) oxidation
The aerobic oxidation of ferrous iron (Fe2+) to ferric iron (Fe3+) supports growth of
chemolithotrophic iron bacteria. However, at acidic pH only a small amount of energy is available
from this reaction.
Because the reduction potential of the Fe2+/Fe3+ couple is so high, steps in electron transport to
oxygen can obviously be few. Iron oxidation begins in the outer membrane where the organism
contacts ferrous iron which is than oxidised to ferric iron which is a one electron transition. This
reaction is thought to be pulled forward by the consumption of ferric iron in Fe(OH)3 formation.
The nature of the proton motive force in highly acidic environments is interesting because a large
gradient of protons already exists across the cytoplasmic membrane. However, the organism cannot
make ATP from this preformed proton motive force in the absence of an electron donor. This is
because H+ ions that enter the cytoplasm via ATPase must be consumed in order to maintain the
internal pH within acceptable limits.
Autotrophy is supported by the Calvin cycle and because the high potential of the electron donor,
much energy must be consumed in revere electron flow reactions to obtain the reducing power
(NADH) to drive the CO2 fixation.
Ferrous iron can also be oxidised under anoxic conditions in which Fe2+ is used either as an electron
donor in energy metabolism and/or as a reductant for CO2 fixation.
14.11 Nitrification
Nitrification is the process in which nitrifying bacteria oxidise ammonia and nitrite. Nitrification
consists of two different sets of reactions:
1. Catalyse oxidation of ammonia to nitrite
2. Catalyse oxidation of nitrite to nitrate
Most nitrifying microbes are only capable of catalysing one of the two reactions mentioned above.
The bioenergetics of nitrification is based on the same principles that govern other
chemolithotrophic reactions: electrons from reduced inorganic substrates enter an ETC and electron
transport reactions establish a pmf that drives ATP synthesis. The complete oxidation of NH3 to NO3-
involves an eight electron transfer and the electron donors for the nitrifying bacteria are not
particularly strong.
NH3 is oxidised to NH2OH by ammonia monooxygenase (ammonia oxidising bacteria)
NH2OH is oxidised to NO2- by hydroxylamine oxidoreductase (ammonia oxidising bacteria)
NO2- is oxidised to NO3- by nitrite oxidoreductase (nitrite oxidising bacteria)
Like sulfur- and iron-oxidising chemolithotrophs, aerobic nitrifying bacteria employ the Calvin cycle
for CO2 fixation.
Recall that CO2 fixation is the process by which inorganic carbon is converted to organic compounds.
14.12 Anaerobic Ammonia Oxidation (Anammox)
NH3 can also be oxidised under anaerobic conditions, this process is called anammox.
The anammox reaction is;
