Carbon fixation or сarbon assimilation refers to the conversion process of
inorganic carbon to organic compounds by living organisms. The most prominent
example is photosynthesis, although chemosynthesis is another form of carbon
fixation that can take place in the absence of sunlight. Organisms that grow
by fixing carbon are called autotrophs. Autotrophs include photoautotrophs,
which synthesize organic compounds using the energy of sunlight, and
lithoautotrophs, which synthesize organic compounds using the energy of
inorganic oxidation. Heterotrophs are organisms that grow using the carbon
fixed by autotrophs. The organic compounds are used by heterotrophs to
produce energy and to build body structures. "Fixed carbon", "reduced
carbon", and "organic carbon" are equivalent terms for various organic
compounds. Net vs gross CO2 fixation
It is estimated that approximately 258 billion tons of carbon dioxide are
converted by photosynthesis annually. The majority of the fixation occurs in
marine environments, especially areas of high nutrients. The gross amount of
carbon dioxide fixed is much larger since approximately 40% is consumed by
respiration following photosynthesis. Given the scale of this process, it is
understandable that RuBisCO is the most abundant protein on earth.
Overview of pathways Six autotrophic carbon fixation pathways
are known as of 2011. The Calvin cycle fixes carbon in the chloroplasts of
plants and algae, and in the cyanobacteria. It also fixes carbon in
the anoxygenic photosynthetic proteobacteria called purple bacteria,
and in some non-phototrophic proteobacteria.
Oxygenic photosynthesis In photosynthesis, energy from sunlight
drives the carbon fixation pathway. Oxygenic photosynthesis is used by the
primary producers—plants, algae, and cyanobacteria. They contain the pigment
chlorophyll, and use the Calvin cycle to fix carbon autotrophically. The process
works like this: 2H2O → 4e− + 4H+ + O2
CO2 + 4e− + 4H+ → CH2O + H2O In the first step, water is dissociated
into electrons, protons, and free oxygen. This allows the use of water,
one of the most abundant substances on Earth, as an electron donor—as a source
of reducing power. The release of free oxygen is a side-effect of enormous
consequence. The first step uses the energy of sunlight to oxidize water to
O2, and, ultimately, to produce ATP ADP + Pi ATP + H2O
and the reductant, NADPH NADP+ + 2e− + 2H+ NADPH + H+
In the second step, called the Calvin cycle, the actual fixation of carbon
dioxide is carried out. This process consumes ATP and NADPH. The Calvin cycle
in plants accounts for the preponderance of carbon fixation on land. In algae and
cyanobacteria, it accounts for the preponderance of carbon fixation in the
oceans. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate,
which is glyceraldehyde 3-phosphate together with dihydroxyacetone
phosphate: 3 CO2 + 12 e− + 12 H+ + Pi → TP + 4 H2O
An alternative perspective accounts for NADPH and ATP:
3 CO2 + 6 NADPH + 6 H+ + 9 ATP + 5 H2O → TP + 6 NADP+ + 9 ADP + 8 Pi
The formula for inorganic phosphate is HOPO32− + 2H+. Formulas for triose and
TP are C2H3O2-CH2OH and C2H3O2-CH2OPO32− + 2H+
= Evolutionary considerations = Somewhere between 3.5 and 2.3 billion
years ago, the ancestors of cyanobacteria evolved oxygenic
photosynthesis, enabling the use of the abundant yet relatively oxidized
molecule H2O as an electron donor to the electron tranport chain of
light-catalyzed proton-pumping responsible for efficient ATP synthesis.
When this evolutionary breakthrough occurred, autotrophy is believed to have
already been developed. However, the proliferation of cyanobacteria, due to
their novel ability to exploit water as a source of electrons, radically altered
the global environment by oxygenating the atmosphere and by achieving large
fluxes of CO2 consumption. = Carbon concentrating mechanisms =
Many photosynthetic organisms have acquired inorganic carbon concentrating
mechanisms, which increase the concentration of carbon dioxide
available to the initial carboxylase of the Calvin cycle, the enzyme RuBisCO.
The benefits of CCM include increased tolerance to low external concentrations
of inorganic carbon, and reduced loses to photorespiration. CCM can make plants
more tolerant of heat and water stress. Carbon concentrating mechanisms use the
enzyme carbonic anhydrase, which catalyze both the dehydration of
bicarbonate to carbon dioxide and the hydration of carbon dioxide to
bicarbonate HCO3− + H+ CO2 + H2O
Lipid membranes are much less permeable to bicarbonate than to carbon dioxide.
To capture inorganic carbon more effectively, some plants have adapted
the anaplerotic reactions HCO3− + H+ + PEP → OAA + Pi
catalyzed by PEP carboxylase, to carboxylate phosphoenolpyruvate to
oxaloacetate which is a C4 dicarboxylic acid.
CAM plants CAM plants that use Crassulacean acid
metabolism as an adaptation for arid conditions. CO2 enters through the
stomata during the night and is converted into the 4-carbon compound,
malic acid, which releases CO2 for use in the Calvin cycle during the day, when
the stomata are closed. The jade plant and cacti are typical of CAM plants.
Sixteen thousand species of plants use CAM. These plants have a carbon isotope
signature of -20 to -10 ‰. C4 plants
C4 plants preface the Calvin cycle with reactions that incorporate CO2 into one
of the 4-carbon compounds, malic acid or aspartic acid. C4 plants have a
distinctive internal leaf anatomy. Tropical grasses, such as sugar cane and
maize are C4 plants, but there are many broadleaf plants that are C4. Overall,
7600 species of terrestrial plants use C4 carbon fixation, representing around
3% of all species. These plants have a carbon isotope signature of -16 to -10
‰. C3 plants
The large majority of plants are C3 plants. They are so-called to
distinguish them from the CAM and C4 plants, and because the carboxylation
products of the Calvin cycle are 3-carbon compounds. They lack C4
dicarboxylic acid cycles, and therefore have higher carbon dioxide compensation
points than CAM or C4 plants. C3 plants have a carbon isotope signature of -24
to -33‰. Other autotrophic pathways
Of the five other autotrophic pathways, two are known only in bacteria, two only
in archaea, and one in both bacteria and archaea.
= Reductive citric acid cycle = The reductive citric acid cycle is the
oxidative citric acid cycle run in reverse. It has been found in anaerobic
and microaerobic bacteria. It was proposed in 1966 by Evans, Buchanan and
Arnon who were working with the anoxygenic photosynthetic green sulfur
bacterium that they called Chlorobium thiosulfatophilum. The reductive citric
acid cycle is sometimes called the Arnon-Buchanan cycle.
= Reductive acetyl CoA pathway = The reductive acetyl CoA pathway
operated in strictly anaerobic bacteria and archaea. The pathway was proposed in
1965 by Ljungdahl and Wood. They were working with the gram-positive acetic
acid producing bacterium Clostridium thermoaceticum, which is now named
Moorella thermoacetica. Hydrogenotrophic methanogenesis, which is only found in
certain archaea and accounts fror 80% of global methanogenesis, is also based on
the reductive acetyl CoA pathway. The pathway is often referred to as the
Wood-Ljungdahl pathway. = 3-Hydroxypropionate and two related
cycles = The 3-hydroxypropionate cycle is
utilized only by green nonsulfur bacteria. It was proposed in 2002 for
the anoxygenic photosynthetic Chloroflexus aurantiacus. None of the
enzymes that participate in the 3-hydroxypropionate cycle are especially
oxygen sensitive. A variant of the 3-hydroxypropionate
pathway was found to operate in aerobic extreme thermoacidophile archaeon
Metallosphaera sedula. This pathway, called the
3-hydroxypropionate/4-hydroxybutyrate cycle . And yet another variant of the
3-hydroxypropionate pathway is the dicarboxylate/4-hydroxybutyrate cycle.
It was discovered in anaerobic archaea. It was proposed in 2008 for the
hyperthermophile archeon Ignicoccus hospitalis.
Chemosynthesis Chemosynthesis is carbon fixation driven
by the oxidation of inorganic substances. Sulfur- and
hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric
acid cycle. Non-autotrophic pathways
Although almost all heterotrophs cannot synthesize complete organic molecules
from carbon dioxide, some carbon dioxide is incorporated in their metabolism.
Notably pyruvate carboxylase consumes carbon dioxide as part of
gluconeogenesis, and carbon dioxide is consumed in various anaplerotic
reactions. Carbon isotope discrimination
Some carboxylases, particularly RuBisCO, preferentially bind the lighter carbon
stable isotope carbon-12 over the heavier carbon-13. This is known as
carbon isotope discrimination and results in carbon-12 to carbon-13 ratios
in the plant that are lower than in the free air. Measurement of this ratio is
important in the evaluation of water use efficiency in plants, and also in
assessing the possible or likely sources of carbon in global carbon cycle
studies. References
Further reading