Biological carbon fixation

thumb |alt=Filamentous cyanobacterium |[[Cyanobacteria such as these carry out photosynthesis. Their emergence foreshadowed the evolution of many photosynthetic plants and oxygenated Earth's atmosphere.]]

Biological carbon fixation, or carbon assimilation, is the process by which living organisms convert inorganic carbon (particularly carbon dioxide, ) to organic compounds. These organic compounds are then used to store energy and as structures for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use chemosynthesis in the absence of sunlight. Chemosynthesis is carbon fixation driven by chemical energy rather than from sunlight.

The process of biological carbon fixation plays a crucial role in the global carbon cycle, as it serves as the primary mechanism for removing from the atmosphere and incorporating it into living biomass. The primary production of organic compounds allows carbon to enter the biosphere. The flow of carbon from the Earth's atmosphere, oceans and lithosphere into lifeforms and then back into the air, water and soil is one of the key biogeochemical cycles (or nutrient cycles).

Organisms that grow by fixing carbon, such as most plants and algae, are called autotrophs. These include photoautotrophs (which use sunlight) and lithoautotrophs (which use inorganic oxidation). Heterotrophs, such as animals and fungi, are not capable of carbon fixation but are able to grow by consuming the carbon fixed by autotrophs or other heterotrophs.

Seven natural autotrophic carbon fixation pathways are currently known:

"Fixed carbon," "reduced carbon," and "organic carbon" may all be used interchangeably to refer to various organic compounds.

Net vs. gross CO₂ fixation

600px|thumb|center|Graphic showing net annual amounts of CO₂ fixation by land and sea-based organisms.

The primary form of fixed inorganic carbon is carbon dioxide (CO₂). It is estimated that approximately 250 billion tons of carbon dioxide are converted by photosynthesis annually, nearly one half in the oceans and a bit more in terrestrial environments. The majority of the fixation in terrestrial environments occurs in the tropics. The gross amount of carbon dioxide fixed is much larger since approximately 40% is consumed by respiration following photosynthesis. Historically, it is estimated that approximately 2×10¹¹ billion tons of carbon has been fixed since the origin of life.

Overview of the carbon fixation cycles

Seven autotrophic carbon fixation pathways are known:

Of the other autotrophic pathways, three are known only in bacteria (the reductive citric acid cycle, the 3-hydroxypropionate cycle, and the reductive glycine pathway), two only in archaea (two variants of the 3-hydroxypropionate cycle), and one in both bacteria and archaea (the reductive acetyl CoA pathway). Sulfur- and hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric acid cycle.

List of pathways

thumb|Overview of the Calvin Cycle

Calvin cycle

The Calvin cycle accounts for 90% of biological carbon fixation. Consuming adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH), the Calvin cycle in plants accounts for the predominance of carbon fixation on land. In algae and cyanobacteria, it accounts for the dominance of carbon fixation in the oceans. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate (TP), which is glyceraldehyde 3-phosphate (GAP) together with dihydroxyacetone phosphate (DHAP):

: 3 CO₂ + 12 e⁻ + 12 H⁺ + P_i → TP + 4 H₂O

An alternative perspective accounts for NADPH (source of e⁻) and ATP:

: 3 CO₂ + 6 NADPH + 6 H⁺ + 9 ATP + 5 H₂O → TP + 6 NADP⁺ + 9 ADP + 8 P_i

The formula for inorganic phosphate (P_i) is HOPO₃²⁻ + 2 H⁺.<br />Formulas for triose and TP are C₂H₃O₂-CH₂OH and C₂H₃O₂-CH₂OPO₃²⁻ + 2 H⁺.

<!--=== Evolutionary considerations ===

Somewhere between 3.8 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 transport chain of light-catalyzed proton-pumping responsible for efficient ATP synthesis. When this evolutionary breakthrough occurred, autotrophy (growth using inorganic carbon as the sole carbon source) 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.

CO₂ concentrating mechanisms

Many photosynthetic organisms have not acquired CO₂ concentrating mechanisms (CCMs), which involve a reversible (not net) fixation of CO₂. They operate by PEP carboxylase (PEPC), to carboxylate phosphoenolpyruvate (PEP) to oxaloacetate (OAA) which is a C₄ dicarboxylic acid. CCM's ultimately contribute to the Calvin cycle. Their benefits include increased tolerance to low external concentrations of inorganic carbon, and reduced losses to photorespiration. CCMs can make plants more tolerant of heat and water stress. CCMs use the enzyme carbonic anhydrase (CA), which catalyze both the dehydration of bicarbonate to CO₂ and the hydration of CO₂ to bicarbonate

:HCO₃⁻ + H⁺ CO₂ + H₂O-->

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Lipid membranes are much less permeable to bicarbonate than to CO₂. To capture inorganic carbon more effectively, some plants have adapted the anaplerotic reactions

: HCO₃⁻ + H⁺ + PEP → OAA + P_i

catalyzed

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 dung jade plant (Crassula ovata) 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 ‰. These plants have a carbon isotope signature of −16 to −10 ‰.

Bacteria and cyanobacteria

Almost all cyanobacteria and some bacteria utilize carboxysomes to concentrate carbon dioxide. Carboxysomes are protein shells filled with the enzyme RuBisCO and a carbonic anhydrase. The carbonic anhydrase produces CO₂ from the bicarbonate that diffuses into the carboxysome. The surrounding shell provides a barrier to carbon dioxide loss, helping to increase its concentration around RuBisCO.

Eukaryotic algae

In eukaryotic algae, various bicarbonate transporters and carbonic anhydrases serve to increase the CO₂ flux balance toward the pyrenoid, a low CO₂-permeable subcellular compartment in the chloroplast containing most of the RuBisCO.

== Other autotrophic pathways ==-->class=skin-invert-image|alt=rTCA cycle with the reactants, intermediates, and products|thumb|Reverse Krebs Cycle

Reverse Krebs cycle

The reverse Krebs cycle, also known as the reverse TCA cycle (rTCA) or reductive citric acid cycle, is an alternative to the standard Calvin-Benson cycle for carbon fixation. It has been found in strict anaerobic or microaerobic bacteria (as Aquificales) and anaerobic archea. It was discovered by Evans, Buchanan and Arnon in 1966 working with the photosynthetic green sulfur bacterium Chlorobium limicola. In particular, it is one of the most used pathways in hydrothermal vents by the Campylobacterota. This feature allows primary production in the ocean's aphotic environments, or "dark primary production." Without it, there would be no primary production in aphotic environments, which would lead to habitats without life.

The cycle involves the biosynthesis of acetyl-CoA from two molecules of CO₂.

The bacteria Gammaproteobacteria and Riftia pachyptila switch from the Calvin-Benson cycle to the rTCA cycle in response to concentrations of H₂S.

class=skin-invert-image|thumb|The reductive acetyl-CoA pathway

Reductive acetyl CoA pathway

The reductive acetyl CoA pathway (CoA) pathway, also known as the Wood-Ljungdahl pathway uses CO₂ as electron acceptor and carbon source, and H₂ as an electron donor to form acetic acid. This metabolism is widespread within the phylum Bacillota, especially in the Clostridia. Hydrogenotrophic methanogenesis, which is only found in certain archaea and accounts for 80% of global methanogenesis, is also based on the reductive acetyl CoA pathway.

The Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase is the oxygen-sensitive enzyme that permits the reduction of CO₂ to CO and the synthesis of acetyl-CoA in several reactions.

One branch of this pathway, the methyl branch, is similar but non-homologous between bacteria and archaea. In this branch happens the reduction of CO₂ to a methyl residue bound to a cofactor. The intermediates are formate for bacteria and formyl-methanofuran for archaea, and also the carriers, tetrahydrofolate and tetrahydropterins respectively in bacteria and archaea, are different, such as the enzymes forming the cofactor-bound methyl group. The 3-hydroxypropionate bicycle is composed of two cycles, and the name of this way comes from the 3-hydroxypropionate, which corresponds to an intermediate characteristic of it.

class=skin-invert-image|thumb|191x191px|Part 1

The first cycle is a way of synthesis of glyoxylate. During this cycle, two equivalents of bicarbonate are fixed by the action of two enzymes: the acetyl-CoA carboxylase catalyzes the carboxylation of the acetyl-CoA to malonyl-CoA and propionyl-CoA carboxylase catalyses the carboxylation of propionyl-CoA to methylamalonyl-CoA. From this point, a series of reactions lead to the formation of glyoxylate, which will thus become part of the second cycle.

class=skin-invert-image|thumb|210x210px|Part 2

In the second cycle, glyoxylate is approximately one equivalent of propionyl-CoA forming methylamalonyl-CoA. This, in turn, is then converted through a series of reactions into citramalyl-CoA. The citramalyl-CoA is split into pyruvate and acetyl-CoA thanks to the enzyme MMC lyase. The pyruvate is released at this point, while the acetyl-CoA is reused and carboxylated again at malonyl-CoA, thus reconstituting the cycle.

A total of 19 reactions are involved in the 3-hydroxypropionate bicycle, and 13 multifunctional enzymes are used. The multi-functionality of these enzymes is an important feature of this pathway which thus allows the fixation of three bicarbonate molecules.

Yet another variant of the 3-hydroxypropionate cycle is the dicarboxylate/4-hydroxybutyrate (DC/4-HB) cycle. It was discovered in anaerobic archaea.

It was proposed in 2008 for the hyperthermophile archeon Ignicoccus hospitalis.

Enoyl-CoA carboxylases/reductases

fixation is catalyzed by enoyl-CoA carboxylases/reductases.

Non-autotrophic pathways

Although no heterotrophs use carbon dioxide in biosynthesis, some carbon dioxide is incorporated in their metabolism. Notably pyruvate carboxylase consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis, and carbon dioxide is consumed in various anaplerotic reactions.

6-phosphogluconate dehydrogenase catalyzes the reductive carboxylation of ribulose 5-phosphate to 6-phosphogluconate in E. coli under elevated CO₂ concentrations.

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 higher than in the free air. Measurement of this isotopic 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.

Biological carbon fixation in soils

In addition to photosynthetic and chemosynthetic processes, biological carbon fixation occurs in soil through the activity of microorganisms, such as bacteria and fungi. These soil microbes play a crucial role in the global carbon cycle by sequestering carbon from decomposed organic matter and recycling it back into the soil, thereby contributing to soil fertility and ecosystem productivity. These substances help bind together soil particles, forming aggregates that protect organic carbon from microbial decomposition and physical erosion. Over time, these aggregates accumulate in the soil, forming soil organic matter, which can persist for centuries to millennia.

The sequestration of carbon in soil not only helps mitigate the accumulation of atmospheric and mitigate climate change but also enhances soil fertility, water retention, and nutrient cycling, thereby supporting plant growth and ecosystem productivity. Consequently, understanding the role of soil microbes in biological carbon fixation is essential for managing soil health, mitigating climate change, and promoting sustainable land management practices.

Biological carbon fixation is a fundamental process that sustains life on Earth by regulating atmospheric levels, supporting the growth of plants and other photosynthetic organisms, and maintaining ecological balance.

See also

• Blue carbon
• Nitrogen fixation
• Oxygen cycle
• Biogeochemical cycles

References

Further reading