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Biological carbon fixation, or сarbon assimilation, is the process by which living organisms convert inorganic carbon (particularly carbon dioxide, ) to Organic compound. These organic compounds are then used to store energy and as structures for other Biomolecule. 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. Carbon is considered essential for life as a base element for building organic compounds. 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 cycle). Understanding biological carbon fixation is essential for comprehending ecosystem dynamics, climate regulation, and the sustainability of life on Earth.
Organisms that grow by fixing carbon, such as most plants and algae, are called Autotroph. These include Phototroph (which use sunlight) and Lithoautotroph (which use Oxidizing agent). Heterotroph, 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. They are the: i) Calvin-Benson-Bassham (Calvin Cycle), ii) Reverse Krebs (rTCA) cycle, iii) the reductive acetyl-CoA (Wood-Ljungdahl pathway), iv) [3-Hydroxypropionate bicycle]], v) 3-hydroypropionate/4- hydroxybutyrate (3-HP/4-HB) cycle, vi) the dicarboxylate/ 4-hydroxybutyrate (DC/4-HB) cycle, and vii) the reductive glycine (rGly) pathway. "Fixed carbon," "reduced carbon," and "organic carbon" may all be used interchangeably to refer to various organic compounds.
The organisms the Calvin cycle is found in are plants, algae, cyanobacteria, aerobic proteobacteria, and purple bacteria. The Calvin cycle fixes carbon in the of plants and algae, and in the cyanobacteria. It also fixes carbon in the anoxygenic photosynthesis in one type of Pseudomonadota called purple bacteria, and in some non-phototrophic Pseudomonadota.
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.
The formula for inorganic phosphate (Pi) is HOPO32− + 2 H+.
Formulas for triose and TP are C2H3O2-CH2OH and C2H3O2-CH2OPO32− + 2 H+.
The cycle involves the biosynthesis of acetyl-CoA from two molecules of CO2. The key steps of the reverse Krebs cycle are:
This pathway is cyclic due to the regeneration of the oxaloacetate.
The bacteria Gammaproteobacteria and Riftia pachyptila switch from the Calvin-Benson cycle to the rTCA cycle in response to concentrations of Hydrogen sulfide.
The pathway is also used by , which are mainly Euryarchaeota, and several anaerobic chemolithoautotrophs, such as sulfate-reducing bacteria and archaea. It is probably performed also by the Brocadiales, an order of Planctomycetota that oxidize ammonia in anaerobic conditions. 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.
Otherwise, the carbonyl branch is homologous between the two domains and consists of the reduction of another molecule of CO2 to a carbonyl residue bound to an enzyme, catalyzed by the CO dehydrogenase/acetyl-CoA synthase. This key enzyme is also the catalyst for the formation of acetyl-CoA starting from the products of the previous reactions, the methyl and the carbonyl residues.
This carbon fixation pathway requires only one molecule of ATP for the production of one molecule of pyruvate, which makes this process one of the main choice for chemolithoautotrophs limited in energy and living in anaerobic conditions.
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.
It is a costly pathway: 7 ATP molecules are consumed to synthesise the new pyruvate and 3 ATP for the phosphate triose.
An important characteristic of this cycle is that it allows the co-assimilation of numerous compounds, making it suitable for the organisms.
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.
fixation is catalyzed by enoyl-CoA carboxylases/reductases.
6-phosphogluconate dehydrogenase catalyzes the reductive carboxylation of ribulose 5-phosphate to 6-phosphogluconate in E. coli under elevated CO2 concentrations.
In soil environments, organic matter derived from dead plant and animal material undergoes decomposition, a process carried out by a diverse community of microorganisms. During decomposition, complex organic compounds are broken down into simpler molecules by the action of enzymes produced by bacteria, fungi, and other soil organisms. As organic matter is decomposed, carbon is released in various forms, including carbon dioxide () and dissolved organic carbon (DOC).
However, not all the carbon released during decomposition is immediately lost to the atmosphere; a significant portion is retained in the soil through processes collectively known as soil carbon sequestration. Soil microbes, mainly bacteria and fungi, play a pivotal role in this process by incorporating decomposed organic carbon into their biomass or by facilitating the formation of stable organic compounds, such as humus and soil organic matter.
One key mechanism by which soil microbes sequester carbon is through microbial biomass production. Bacteria and fungi assimilate carbon from decomposed organic matter into their cellular structures as they grow and reproduce. This microbial biomass serves as a reservoir for stored carbon in the soil, effectively sequestering carbon from the atmosphere.
Additionally, soil microbes contribute to the formation of stable soil organic matter through the synthesis of extracellular polymers, , and other biochemical compounds. LibreTexts Biology, 3.4: Biochemical compounds These substances help bind together soil particles, Soil Science Society of America (SSSA). Physical Properties of Soil – Soil Texture 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 Photoautotroph, and maintaining ecological balance.
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