Biological carbon fixation

{{Short description|Series of interconnected biochemical reactions}} {{Other uses|Carbon cycle|Carbon sequestration}} {{Redirect|Fixed carbon|the component of coal|Coal analysis}} {{cs1 config|name-list-style=vanc|display-authors=6}} {{Use dmy dates|date=June 2020}} [[File:20100422 235222 Cyanobacteria.jpg|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, {{chem2|CO2}}) 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 {{chem2|CO2}} from the atmosphere and incorporating it into living biomass. The primary production of organic compounds allows carbon to enter the biosphere.<ref name=":52"/> Carbon is considered essential for life as a base element for building organic compounds.<ref name=":52">{{Cite journal |last1=Santos Correa |first1=Sulamita |last2=Schultz |first2=Junia |last3=Lauersen |first3=Kyle J. |last4=Soares Rosado |first4=Alexandre |date=2023-05-01 |title=Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways |journal=Journal of Advanced Research |volume=47 |pages=75–92 |doi=10.1016/j.jare.2022.07.011 |pmid=35918056 |pmc=10173188 |issn=2090-1232|hdl=10754/680126 |hdl-access=free }}</ref> 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).<ref name=":52"/> Understanding biological carbon fixation is essential for comprehending [https://www.turito.com/learn/biology/ecosystem-dynamics-grade-8 ecosystem dynamics], climate regulation, and the sustainability of life on Earth.<ref name="Berg2013">{{Cite book |last1=Berg |first1=Jeremy M. |last2=Tymoczko |first2=John L. |last3=Stryer |first3=Lubert |date=2013 |title=Stryer Biochemie |doi=10.1007/978-3-8274-2989-6|isbn=978-3-8274-2988-9}}</ref>

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:<ref name=":52"/><ref>{{cite journal |last1=Bierbaumer |first1=Sarah |last2=Nattermann |first2=Maren |last3=Schulz |first3=Luca |last4=Zschoche |first4=Reinhard |last5=Erb |first5=Tobias |last6=Winkler |first6=Christoph |last7=Tinzl |first7=Matthias |last8=Glueck |first8=Silvia |title=Enzymatic Conversion of CO₂: From Natural to Artificial Utilization |journal=Chemical Reviews |date=2023-01-24 |volume=123 |issue=9 |pages=5702–5754 |doi=10.1021/acs.chemrev.2c00581|pmid=36692850 |pmc=10176493 }}</ref> {{bulleted list |Calvin-Benson-Bassham cycle (Calvin Cycle)|Reverse Krebs cycle (rTCA)|Wood-Ljungdahl pathway (reductive acetyl-CoA pathway)|3-Hydroxypropionate bicycle (3-HP bicycle)|3-Hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle)|dicarboxylate/4-hydroxybutyrate cycle (DC/4-HB cycle)|reductive glycine pathway (rGly)}} "Fixed carbon," "reduced carbon," and "organic carbon" may all be used interchangeably to refer to various organic compounds.<ref name="Geider2">{{cite journal |vauthors=Geider RJ, et al |year=2001 |title=Primary productivity of planet earth: biological determinants and physical constraints in terrestrial and aquatic habitats |journal=Global Change Biology |volume=7 |issue=8 |pages=849–882 |bibcode=2001GCBio...7..849G |doi=10.1046/j.1365-2486.2001.00448.x |s2cid=41335311 |doi-access=free}}</ref>

== 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.<ref name=Geider>{{cite journal | vauthors = Geider RJ, et al | year = 2001 | title = Primary productivity of planet earth: biological determinants and physical constraints in terrestrial and aquatic habitats | journal = Global Change Biology | volume = 7 | issue = 8 | pages = 849–882 | doi = 10.1046/j.1365-2486.2001.00448.x | bibcode = 2001GCBio...7..849G | s2cid = 41335311 | doi-access = free }}</ref><ref>Raghavendra, A. S. (2003-01-01), Thomas, Brian (ed.), "Photosynthesis and Partitioning | C3 Plants", ''Encyclopedia of Applied Plant Sciences'', Oxford: Elsevier, pp. 673–680, {{ISBN|978-0-12-227050-5}}, retrieved 2021-03-21</ref> Historically, it is estimated that approximately 2×10¹¹ billion tons of carbon has been fixed since the origin of life.<ref>{{cite journal |last1=Crockford |first1=Peter W. |last2=Bar On |first2=Yinon M. |last3=Ward |first3=Luce M. |last4=Milo |first4=Ron |last5=Halevy |first5=Itay |date=November 2023 |title=The geologic history of primary productivity |journal=Current Biology |volume=33 |issue=21 |pages=4741–4750.e5 |doi=10.1016/j.cub.2023.09.040 |pmid=37827153 |bibcode=2023CBio...33E4741C |s2cid=263839383 |issn=0960-9822|doi-access=free }}</ref>

== Overview of the carbon fixation cycles == Seven autotrophic carbon fixation pathways are known:<ref name=":52"/> the Calvin Cycle, the Reverse Krebs Cycle, the reductive acetyl-CoA, the 3-HP bicycle, the 3-HP/4-HB cycle, the DC/4-HB cycles, and the reductive glycine pathway.

thumb|416x416px|Overview of the six known biological carbon fixation cycles|alt=Overview of the six known biological carbon fixation cycles|center

The organisms the Calvin cycle is found in are plants, algae, cyanobacteria, aerobic proteobacteria, and purple bacteria.<ref name=":52"/> The Calvin cycle fixes carbon in the chloroplasts 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.<ref name="Swan11"> {{cite journal | vauthors = Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland ED, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R | title = Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean | journal = Science | volume = 333 | issue = 6047 | pages = 1296–300 | date = September 2011 | pmid = 21885783 | doi = 10.1126/science.1203690 | s2cid = 206533092 | bibcode = 2011Sci...333.1296S }} </ref>

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.<ref>{{cite book |url=https://books.google.com/books?id=rLhdW5YzuO4C&q=chemosynthesis+carbon+fixation&pg=RA2-PA83 |title=Encyclopedia of Microbiology |publisher=Academic Press |year=2009 |isbn=978-0-12-373944-5 |pages=83–84}}</ref>

== 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):<ref>{{Cite journal |last=Raines |first=Christine A. |date=2003-01-01 |title=The Calvin cycle revisited |journal=Photosynthesis Research |language=en |volume=75 |issue=1 |pages=1–10 |doi=10.1023/A:1022421515027 |pmid=16245089 |bibcode=2003PhoRe..75....1R |issn=1573-5079}}</ref> : 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,<ref>{{cite journal | vauthors = Cardona T, Sánchez-Baracaldo P, Rutherford AW, Larkum AW | title = Early Archean origin of Photosystem II | journal = Geobiology | volume = 17 | issue = 2 | pages = 127–150 | date = March 2019 | pmid = 30411862 | pmc = 6492235 | doi = 10.1111/gbi.12322 }}</ref><ref>{{cite journal | vauthors = Cardona T, Murray JW, Rutherford AW | title = Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria | journal = Molecular Biology and Evolution | volume = 32 | issue = 5 | pages = 1310–28 | date = May 2015 | pmid = 25657330 | pmc = 4408414 | doi = 10.1093/molbev/msv024 }}</ref> 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.<ref name="Brasier06"> {{cite journal | vauthors = Brasier M, McLoughlin N, Green O, Wacey D | title = A fresh look at the fossil evidence for early Archaean cellular life | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 361 | issue = 1470 | pages = 887–902 | date = June 2006 | pmid = 16754605 | pmc = 1578727 | doi = 10.1098/rstb.2006.1835 }} </ref><ref name="Tomitani06">{{cite journal | vauthors = Tomitani A, Knoll AH, Cavanaugh CM, Ohno T | title = The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 14 | pages = 5442–7 | date = April 2006 | pmid = 16569695 | pmc = 1459374 | doi = 10.1073/pnas.0600999103 | bibcode = 2006PNAS..103.5442T | doi-access = free }} </ref> 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.<ref name="Kopp05"> {{cite journal | vauthors = Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ | title = The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 32 | pages = 11131–6 | date = August 2005 | pmid = 16061801 | pmc = 1183582 | doi = 10.1073/pnas.0504878102 | bibcode = 2005PNAS..10211131K | doi-access = free }}</ref> ===CO₂ concentrating mechanisms=== {{anchor|carbon dioxide-concentrating mechanism}} 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⁺ {{eqm}} CO₂ + H₂O--> <!-- 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.<ref name="Dodd02"> {{cite journal | vauthors = Dodd AN, Borland AM, Haslam RP, Griffiths H, Maxwell K | title = Crassulacean acid metabolism: plastic, fantastic | journal = Journal of Experimental Botany | volume = 53 | issue = 369 | pages = 569–80 | date = April 2002 | pmid = 11886877 | doi = 10.1093/jexbot/53.369.569 | doi-access = free }} </ref> These plants have a carbon isotope signature of −20 to −10 ‰.<ref name="O'Leary88"/>

==== 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.<ref name="Sage99"> {{cite book |veditors=Sage RF, Monson RK |vauthors=Sage RF, Meirong L, Monson RK |title=C4 Plant Biology |year=1999 |pages=551–580 |chapter=16. The Taxonomic Distribution of C4 Photosynthesis |isbn=0-12-614440-0}} </ref> These plants have a carbon isotope signature of −16 to −10 ‰.<ref name="O'Leary88"/>

==== 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 CO₂ compensation points than CAM or C₄ plants. C₃ plants have a carbon isotope signature of −24 to −33‰.<ref name="O'Leary88"> {{cite journal |author=O'Leary MH |s2cid=29110460 |title=Carbon isotopes in photosynthesis |jstor=1310735 |journal=BioScience |volume=38 |issue=5 |pages=328–336 |year=1988 |doi=10.2307/1310735}} </ref>

==== Bacteria and cyanobacteria ==== Almost all cyanobacteria and some bacteria utilize carboxysomes to concentrate carbon dioxide.<ref>{{cite journal|last=Badger|first=M. R.|date=2003-02-01|title=CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution|journal=Journal of Experimental Botany|volume=54|issue=383|pages=609–622|doi=10.1093/jxb/erg076|pmid=12554704|doi-access=free}}</ref> 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 <ref>{{cite journal|last1=Pierella Karlusich|first1=Juan José|last2=Bowler|first2=Chris|last3=Biswas|first3=Haimanti|date=2021-04-30|title=Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans|journal=Frontiers in Plant Science|volume=12|article-number=657821|doi=10.3389/fpls.2021.657821|issn=1664-462X|pmc=8119650|pmid=33995455|doi-access=free}}</ref> serve to increase the CO₂ flux balance toward the pyrenoid, a low CO₂-permeable subcellular compartment in the chloroplast containing most of the RuBisCO.<ref>{{cite journal|last1=Hennacy|first1=Jessica H.|last2=Jonikas|first2=Martin C.|date=2020-04-29|title=Prospects for Engineering Biophysical CO 2 Concentrating Mechanisms into Land Plants to Enhance Yields|journal=Annual Review of Plant Biology|language=en|volume=71|issue=1|pages=461–485|doi=10.1146/annurev-arplant-081519-040100|issn=1543-5008|pmc=7845915|pmid=32151155}}</ref><ref>{{cite journal|last1=Meyer|first1=Moritz T|last2=Whittaker|first2=Charles|last3=Griffiths|first3=Howard|date=2017-06-22|title=The algal pyrenoid: key unanswered questions|url=http://academic.oup.com/jxb/article/68/14/3739/3858331/The-algal-pyrenoid-key-unanswered-questions|journal=Journal of Experimental Botany|language=en|volume=68|issue=14|pages=3739–3749|doi=10.1093/jxb/erx178|pmid=28911054|issn=0022-0957}}</ref>

== 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''.<ref>{{cite journal | vauthors = Fuchs G | title = Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? | journal = Annual Review of Microbiology | volume = 65 | issue = 1 | pages = 631–58 | date = 2011-10-13 | pmid = 21740227 | doi = 10.1146/annurev-micro-090110-102801 }}</ref> In particular, it is one of the most used pathways in hydrothermal vents by the Campylobacterota.<ref>{{cite journal | vauthors = Grzymski JJ, Murray AE, Campbell BJ, Kaplarevic M, Gao GR, Lee C, Daniel R, Ghadiri A, Feldman RA, Cary SC | title = Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 45 | pages = 17516–21 | date = November 2008 | pmid = 18987310 | pmc = 2579889 | doi = 10.1073/pnas.0802782105 | bibcode = 2008PNAS..10517516G | doi-access = free }}</ref> This feature allows primary production in the ocean's aphotic environments, or "dark primary production."<ref name=":3">{{cite journal |vauthors=Baltar F, Herndl GJ |date=2019-06-11 |title=Is dark carbon fixation relevant for oceanic primary production estimates? |url=https://www.biogeosciences-discuss.net/bg-2019-223/bg-2019-223.pdf |journal=Biogeosciences |doi=10.5194/bg-2019-223 |doi-access=free}}</ref> 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.<ref name=":2"/> The key steps of the reverse Krebs cycle are:

* Oxaloacetate to malate, using NADH + H⁺ *: {{chem2|Oxaloacetate + NADH/H+ -> Malate + NAD+}} * Fumarate to succinate, catalyzed by an oxidoreductase, Fumarate reductase *: {{chem2|Fumarate + FADH2 <-> Succinate + FAD}} * Succinate to succinyl-CoA, an ATP-dependent step *: {{chem2|Succinate + ATP + CoA -> Succinyl\-CoA + ADP + Pi}} * Succinyl-CoA to alpha-ketoglutarate, using one molecule of CO₂ *: {{chem2|Succinyl\-CoA + CO2 + Fd_{(red)} -> alpha\-ketoglutarate + Fd_{(ox)} }} * Alpha-ketoglutarate to isocitrate, using NADPH + H⁺ and another molecule of CO₂ *: {{chem2|Alpha\-ketoglutarate + CO2 + NAD(P)H/H+ -> Isocitrate + NAD(P)+}} * Citrate converted into oxaloacetate and acetyl-CoA, this is an ATP dependent step and the key enzyme is the ATP citrate lyase *: {{chem2|Citrate + ATP + CoA -> Oxaloacetate + Acetyl\-CoA + ADP + Pi}}

This pathway is cyclic due to the regeneration of the oxaloacetate.<ref>{{cite journal | vauthors = Buchanan BB, Arnon DI | title = A reverse Krebs cycle in photosynthesis: consensus at last | journal = Photosynthesis Research | volume = 24 | issue = 1 | pages = 47–53 | date = April 1990 | pmid = 24419764 | doi = 10.1007/bf00032643 | bibcode = 1990PhoRe..24...47B | s2cid = 2753977 }}</ref>

The bacteria Gammaproteobacteria and ''Riftia pachyptila'' switch from the Calvin-Benson cycle to the rTCA cycle in response to concentrations of H₂S.<ref>{{cite journal | vauthors = Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hügler M, Albrecht D, Robidart J, Bench S, Feldman RA, Hecker M, Schweder T | title = Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila | journal = Science | volume = 315 | issue = 5809 | pages = 247–50 | date = January 2007 | pmid = 17218528 | doi = 10.1126/science.1132913 | hdl-access = free | s2cid = 45745396 | bibcode = 2007Sci...315..247M | oclc = 655249163 | hdl = 1912/1514 }}</ref> 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.<ref>{{cite journal | vauthors = Ljungdahl LG | title = A life with acetogens, thermophiles, and cellulolytic anaerobes | journal = Annual Review of Microbiology | volume = 63 | issue = 1 | pages = 1–25 | date = 2009 | pmid = 19575555 | doi = 10.1146/annurev.micro.091208.073617 | doi-access = free }}</ref> This metabolism is widespread within the phylum Bacillota, especially in the Clostridia.<ref name=":0" />

The pathway is also used by methanogens, 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.<ref name=":2">{{cite journal | vauthors = Hügler M, Sievert SM | title = Beyond the Calvin cycle: autotrophic carbon fixation in the ocean | journal = Annual Review of Marine Science | volume = 3 | issue = 1 | pages = 261–89 | date = 2011-01-15 | pmid = 21329206 | doi = 10.1146/annurev-marine-120709-142712 | s2cid = 44800487 | bibcode = 2011ARMS....3..261H }}</ref><ref name=":0">{{cite journal | vauthors = Drake HL, Gössner AS, Daniel SL | title = Old acetogens, new light | journal = Annals of the New York Academy of Sciences | volume = 1125 | issue = 1 | pages = 100–28 | date = March 2008 | pmid = 18378590 | doi = 10.1196/annals.1419.016 | s2cid = 24050060 | bibcode = 2008NYASA1125..100D }}</ref><ref>{{cite journal | vauthors = Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, Le Paslier D | title = Deciphering the evolution and metabolism of an anammox bacterium from a community genome | journal = Nature | volume = 440 | issue = 7085 | pages = 790–4 | date = April 2006 | pmid = 16598256 | doi = 10.1038/nature04647 | s2cid = 4402553 | bibcode = 2006Natur.440..790S | hdl = 2066/35981 | hdl-access = free }}</ref> 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.<ref name=":1">{{cite journal | vauthors = Pezacka E, Wood HG | title = Role of carbon monoxide dehydrogenase in the autotrophic pathway used by acetogenic bacteria | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 81 | issue = 20 | pages = 6261–5 | date = October 1984 | pmid = 6436811 | pmc = 391903 | doi = 10.1073/pnas.81.20.6261 | doi-access = free | bibcode = 1984PNAS...81.6261P }}</ref>

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.<ref name=":2"/>

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.<ref name=":1" />

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.<ref name=":2" />

=== 3-Hydroxypropionate (3-HP) bicycle === {{main|3-Hydroxypropionate bicycle}}

The 3-hydroxypropionate bicycle, also known as 3-HP/malyl-CoA cycle, discovered only in 1989, is utilized by green non-sulfur phototrophs of Chloroflexaceae family, including the maximum exponent of this family ''Chloroflexus auranticus'' by which this way was discovered and demonstrated.<ref>{{cite journal | vauthors = Strauss G, Fuchs G | title = Enzymes of a novel autotrophic CO₂ fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle | journal = European Journal of Biochemistry | volume = 215 | issue = 3 | pages = 633–43 | date = August 1993 | pmid = 8354269 | doi = 10.1111/j.1432-1033.1993.tb18074.x | doi-access = free }}</ref> 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.<ref>{{cite journal | vauthors = Herter S, Busch A, Fuchs G | title = L-Malyl-coenzyme A lyase/beta-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO₂ fixation | journal = Journal of Bacteriology | volume = 184 | issue = 21 | pages = 5999–6006 | date = November 2002 | pmid = 12374834 | pmc = 135395 | doi = 10.1128/jb.184.21.5999-6006.2002 }}</ref><ref name=":02">{{cite journal | vauthors = Berg IA | title = Ecological aspects of the distribution of different autotrophic CO₂ fixation pathways | journal = Applied and Environmental Microbiology | volume = 77 | issue = 6 | pages = 1925–36 | date = March 2011 | pmid = 21216907 | pmc = 3067309 | doi = 10.1128/aem.02473-10 | bibcode = 2011ApEnM..77.1925B }}</ref> 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.<ref name="Zarzycki 21317–21322">{{cite journal | vauthors = Zarzycki J, Brecht V, Müller M, Fuchs G | title = Identifying the missing steps of the autotrophic 3-hydroxypropionate CO₂ fixation cycle in Chloroflexus aurantiacus | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 50 | pages = 21317–22 | date = December 2009 | pmid = 19955419 | pmc = 2795484 | doi = 10.1073/pnas.0908356106 | doi-access = free }}</ref>

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.<ref name="Zarzycki 21317–21322"/>

It is a costly pathway: 7 ATP molecules are consumed to synthesise the new pyruvate and 3 ATP for the phosphate triose.<ref name=":02" />

An important characteristic of this cycle is that it allows the co-assimilation of numerous compounds, making it suitable for the mixotrophic organisms.<ref name=":02" />

=== Cycles related to the 3-hydroxypropionate cycle === A variant of the 3-hydroxypropionate cycle was found to operate in the aerobic extreme thermoacidophile archaeon ''Metallosphaera sedula''. This pathway is called the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle.<ref name="Berg07">{{cite journal | vauthors = Berg IA, Kockelkorn D, Buckel W, Fuchs G | title = A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea | journal = Science | volume = 318 | issue = 5857 | pages = 1782–6 | date = December 2007 | pmid = 18079405 | doi = 10.1126/science.1149976 | s2cid = 13218676 | bibcode = 2007Sci...318.1782B }}</ref>

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''.<ref name="Huber08"> {{cite journal | vauthors = Huber H, Gallenberger M, Jahn U, Eylert E, Berg IA, Kockelkorn D, Eisenreich W, Fuchs G | title = A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 22 | pages = 7851–6 | date = June 2008 | pmid = 18511565 | pmc = 2409403 | doi = 10.1073/pnas.0801043105 | bibcode = 2008PNAS..105.7851H | doi-access = free }}</ref>

=== Enoyl-CoA carboxylases/reductases === {{CO2}} fixation is catalyzed by enoyl-CoA carboxylases/reductases.<ref>{{cite journal |doi=10.1126/science.aah5237|title=A synthetic pathway for the fixation of carbon dioxide in vitro|year=2016|last1=Schwander|first1=Thomas|last2=Schada von Borzyskowski|first2=Lennart|last3=Burgener|first3=Simon|last4=Cortina|first4=Niña Socorro|last5=Erb|first5=Tobias J.|journal=Science|volume=354|issue=6314|pages=900–904|pmid=27856910|pmc=5892708|bibcode=2016Sci...354..900S}}</ref>

== Non-autotrophic pathways == Although no heterotrophs use carbon dioxide in biosynthesis, some carbon dioxide is incorporated in their metabolism.<ref>{{cite journal |author1=Nicole Kresge |author2=Robert D. Simoni |author3=Robert L. Hill |title=The Discovery of Heterotrophic Carbon Dioxide Fixation by Harland G. Wood |journal=The Journal of Biological Chemistry |volume=280 |issue=18 |pages=e15 |year=2005 |url=http://www.jbc.org/content/280/18/e15.full}}</ref> 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.<ref>{{cite journal | vauthors = Satanowski A, Dronsella B, Noor E, Vögeli B, He H, Wichmann P, Erb TJ, Lindner SN, Bar-Even A | title = Awakening a latent carbon fixation cycle in Escherichia coli | journal = Nature Communications | volume = 11 | issue = 1 | article-number = 5812 | date = November 2020 | pmid = 33199707 | pmc = 7669889 | doi = 10.1038/s41467-020-19564-5 | bibcode = 2020NatCo..11.5812S | url = }}</ref>

== 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,<ref>{{cite journal | vauthors = Adiredjo AL, Navaud O, Muños S, Langlade NB, Lamaze T, Grieu P | title = Genetic control of water use efficiency and leaf carbon isotope discrimination in sunflower (Helianthus annuus L.) subjected to two drought scenarios | journal = PLOS ONE | volume = 9 | issue = 7 | article-number = e101218 | date = 3 July 2014 | pmid = 24992022 | pmc = 4081578 | doi = 10.1371/journal.pone.0101218 | bibcode = 2014PLoSO...9j1218A | doi-access = free }}</ref><ref>{{cite journal | vauthors = Farquhar GD, Ehleringer JR, Hubick KT |s2cid=12988287 |title=Carbon Isotope Discrimination and Photosynthesis |journal=Annual Review of Plant Physiology and Plant Molecular Biology |date=June 1989 |volume=40 |issue=1 |pages=503–537 |doi=10.1146/annurev.pp.40.060189.002443}}</ref><ref>{{cite journal | vauthors = Seibt U, Rajabi A, Griffiths H, Berry JA | title = Carbon isotopes and water use efficiency: sense and sensitivity | journal = Oecologia | volume = 155 | issue = 3 | pages = 441–54 | date = March 2008 | pmid = 18224341 | doi = 10.1007/s00442-007-0932-7 | s2cid = 451126 | bibcode = 2008Oecol.155..441S }}</ref> 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.<ref name="Berg2013" />

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 ({{CO2}}) 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.<ref name="Berg2013" />

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, enzymes, and other biochemical compounds.<ref name="LibreTextsBiology">[https://bio.libretexts.org/Bookshelves/Human_Biology/Human_Biology_(Wakim_and_Grewal)/03%3A_Chemistry_of_Life/3.04%3A_Biochemical_Compounds LibreTexts Biology, 3.4: Biochemical compounds]</ref> These substances help bind together soil particles,<ref name="SSSA">[https://www.soils4teachers.org/physical-properties/#:~:text=The%20particles%20that%20make%20up,what%20give%20soil%20its%20texture. Soil Science Society of America (SSSA). Physical Properties of Soil – Soil Texture]</ref> 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 {{CO2}} 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 {{CO2}} 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 == {{Reflist}}

== Further reading == {{refbegin}} * {{cite journal | vauthors = Keeling PJ | title = Diversity and evolutionary history of plastids and their hosts | journal = American Journal of Botany | volume = 91 | issue = 10 | pages = 1481–93 | date = October 2004 | pmid = 21652304 | doi = 10.3732/ajb.91.10.1481 | bibcode = 2004AmJB...91.1481K | s2cid = 17522125 | doi-access = free }} * {{cite journal | vauthors = Keeling PJ | title = Chromalveolates and the evolution of plastids by secondary endosymbiosis | journal = The Journal of Eukaryotic Microbiology | volume = 56 | issue = 1 | pages = 1–8 | year = 2009 | pmid = 19335769 | doi = 10.1111/j.1550-7408.2008.00371.x | url = http://www.botany.ubc.ca/keeling/PDF/09KeelingTCS.pdf | s2cid = 34259721 | archive-url = https://wayback.archive-it.org/all/20090709152802/http://www.botany.ubc.ca/keeling/PDF/09KeelingTCS.pdf | archive-date = 9 July 2009 }} * {{cite journal | vauthors = Keeling PJ | title = The endosymbiotic origin, diversification and fate of plastids | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 365 | issue = 1541 | pages = 729–48 | date = March 2010 | pmid = 20124341 | pmc = 2817223 | doi = 10.1098/rstb.2009.0103 }} * {{cite journal | vauthors = Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JA, Lang BF, Burger G, Steiner JM, Löffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MC, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D | title = Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants | journal = Science | volume = 335 | issue = 6070 | pages = 843–7 | date = February 2012 | pmid = 22344442 | doi = 10.1126/science.1213561 | url = http://cels.uri.edu/bio/lanelab/docs/Nic%20docs/PriceEtAl2012.pdf | bibcode = 2012Sci...335..843P | s2cid = 17190180 | archive-url = https://web.archive.org/web/20130514172202/http://cels.uri.edu/bio/lanelab/docs/Nic%20docs/PriceEtAl2012.pdf | archive-date = 14 May 2013 }} * {{cite journal | vauthors = Spiegel FW | title = Evolution. Contemplating the first Plantae | journal = Science | volume = 335 | issue = 6070 | pages = 809–10 | date = February 2012 | pmid = 22344435 | doi = 10.1126/science.1218515 | bibcode = 2012Sci...335..809S | s2cid = 36584136 }} * {{cite journal | vauthors = Timme RE, Bachvaroff TR, Delwiche CF | title = Broad phylogenomic sampling and the sister lineage of land plants | journal = PLOS ONE | volume = 7 | issue = 1 | article-number = e29696 | year = 2012 | pmid = 22253761 | pmc = 3258253 | doi = 10.1371/journal.pone.0029696 | bibcode = 2012PLoSO...729696T | doi-access = free }} {{refend}}

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Category:Photosynthesis Category:Carbon Category:Metabolic pathways Category:Atmospheric chemistry Category:Microbiology