15: Fixing Carbon Fixation
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(Learning goals written by Claude, Anthropic)
By the end of this chapter, students should be able to:
RuBisCO Limitations and Natural Carbon Fixation Pathways
- Explain why RuBisCO is both essential and problematic — describing its slow kcat (2–10 CO₂/sec), large hetero-16-mer structure requiring chaperonin folding, competing oxygenase activity driving photorespiration, and why planting trees cannot solve near-term atmospheric CO₂ problems.
- Compare the six naturally occurring carbon fixation pathways (CBB, reverse TCA, Wood–Ljungdahl, 3-HP, HP/HB, DC/HB) using the summary table, identifying the organisms, energy sources, key enzymes, and products of each, and distinguish photoautotrophic, chemolithoautotrophic, and chemoorganotrophic modes.
Engineered Carbon Fixation: CETCH, rGPS–MCG, and Autotrophic E. coli
- Describe how carbonic anhydrase (kcat/KM up to 8 × 10⁷ M⁻¹s⁻¹) could be engineered for CO₂ capture by addressing reversibility, HCO₃⁻ product inhibition, and thermal instability, and explain how CO₂ mineralization as carbonate precipitate with divalent cations achieves carbon sequestration.
- Describe the CETCH pathway's overall reaction (2CO₂ + 3NAD(P)H + 2ATP + FAD → glycolate + cofactors), explain how it was computationally designed from known CoA-dependent carboxylases, and compare its in vitro CO₂ fixation rate to the Calvin cycle.
- Explain how Gleizer et al. converted E. coli from a heterotroph to a complete autotroph — identifying the genes knocked out (phosphofructokinase, glucose-6-phosphate dehydrogenase), the enzymes added (RuBisCO, phosphoribulokinase, carbonic anhydrase, formate dehydrogenase), the role of formate as an electron donor, and how ¹³CO₂ isotopic labeling confirmed that all biomass carbon derived from CO₂.
- Describe the rGPS–MCG cell-free pathway, explain why a cell-free system offers advantages over living cells (oxygen insensitivity, freedom from growth regulation, continuous operation), and identify its primary products (acetyl-CoA, pyruvate, malate).
Microbial Electrosynthesis and Marine Geoengineering
- Explain microbial electrosynthesis (MES) — how electrons from water oxidation at an anode reduce CO₂ at a biocathode biofilm — identify the oxidation state change required to convert CO₂ to formate (2 electrons), and explain what would make pathways like CETCH truly carbon-neutral.
- Describe the ocean alkalinity enhancement approach (adding crushed limestone to rivers → HCO₃⁻ → marine shell formation → CaCO₃ sinking) and ocean iron fertilization (OIF) (adding FeSO₄ to stimulate phytoplankton CO₂ uptake), and identify the key practical and ecological challenges that make both approaches controversial.
Biological Carbon Fixation
Nature has produced many enzymes that can fix atmospheric CO2, and, of course, everyone knows that photosynthesis is the source of most fixed CO2 in the biosphere. Plankton, cyanobacteria, algae, and plants are key in removing atmospheric CO2 through photosynthesis. Yet, we can't plant enough trees to reduce CO2 in the atmosphere in the next decade to avoid some of the worst consequences of anthropogenic climate change. Old-growth trees (mostly gone or under significant stress) are best at removing CO2. New trees would take decades of growth before their effect on carbon drawdown would be consequential. We must also fix carbon dioxide to decrease atmospheric CO2 and make more food!
Carbon (about 100 petagrams) is sequestered yearly in net primary production (carbon fixation into biomolecules). This is split almost equally between land and ocean organisms. The key enzyme in this process is Rubisco in the C3 (Chapter 20.4) and C4/CAM (Chapter 20.5) pathways. The enzyme is large, containing many large subunits and an equivalent number of small ones. A chaperonin is required for folding. It is also a very slow enzyme with a kcat of around 2-10 CO2/sec. In addition, it can bind another substrate, O2, and engage in a competing reaction, photorespiration, as described in Chapter 20.4.
Figure \(\PageIndex{1}\) shows an interactive iCn3D modelof ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301 (1RBL)
Figure \(\PageIndex{1}\): Ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301 (1RBL) (Copyright; author via source). Click the image for a popup or use this external link (long load time): https://structure.ncbi.nlm.nih.gov/i...pxLGgEKR5gCYK8This structure is a hetero 16-mer consisting of 8 small and 8 large chains. The small chains are gray, and the large ones are different colors. Each large subunit contains a bound reaction intermediate analog, 2-carboxyarabinitol 1,5-bisphosphate.
This chapter will focus on improving and designing new ways to capture carbon dioxide and reduce its atmospheric concentration. Remember that the best way to address anthropogenic climate change is to drastically reduce the burning of fossil fuels.
Naturally occurring pathways to fix carbon
(Much of this immediate section derives from the following reference: Natural carbon fixation. Sulamita Santos et al., Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways, Journal of Advanced Research, Volume 47, 2023, Pages 75-92, ISSN 2090-1232, https://doi.org/10.1016/j.jare. Creative Commons license
Six naturally occurring pathways fix carbon. These are illustrated in Figure \(\PageIndex{2}\) below.
Figure \(\PageIndex{2}\): Natural carbon fixation. Sulamita Santos et al.,ibid.
Panel (A) shows the CBB cycle, which we discussed in great detail in Chapter 20.4. The enzymes involved are ribulose-1,5-bisphosphate carboxylase/oxygenase, 3-phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, and ribulose-phosphate epimerase.
Panel (B) shows the reverse (reductive) TCA cycle, which we discussed in Chapter 16.4 in the section on the α-ketoacid pathway—a primordial, prebiotic anabolic "TCA-like" pathway. The enzymes include ATP-citrate lyase, malate dehydrogenase, succinyl-CoA synthetase, ferredoxin (Fd)- dependent 2-oxoglutarate synthase, isocitrate dehydrogenase, and PEP carboxylase.
Panel (C) shows the Wood–Ljungdahl (or reductive Acetyl-CoA) cycle, which we discussed in Chapter 30.1. At the top of the pathway are the acetogens Archaea, and at the bottom are the methanogens Archaea. The enzymes include MPT-methylene tetrahydromethopterin, MFR-methanofuran, THF, tetrahydrofolate.
Panel (D) shows the 3-hydroxypropionate (3HP) cycle. The enzymes include acetyl-CoA carboxylase, propionyl-CoA carboxylase, methylmalonyl-CoA epimerase, succinyl-CoA:(S)-malate-CoA transferase, trifunctional (S)-malyl-CoA, -methylmalyl-CoA, mesaconyl-CoA transferase, mesaconyl-C4-CoA hydratase.
Panel (E) shows the hydroxypropionate/4-hydroxybutyrate (HP/HB) and the dicarboxylate/4-hydroxybutyrate (DC/HB) cycles. The enzymes include pyruvate synthase, PEP-carboxylase, malate dehydrogenase, fumarate hydratase/reductase, acetyl-CoA/propionyl-CoA carboxylase, 3-hydroxypropionate-CoA ligase/dehydratase, methylmalonyl-CoA mutase, succinyl-CoA reductase, 4-hydroxybutyrate-CoA ligase, crotonyl-CoA hydratase, and acetoacetyl-CoA-ketothiolase.
Table \(\PageIndex{1}\) below shows a comparative description of the natural and synthetic carbon fixation pathways.
| Pathway | Organisms | Energy Source | Input | Output | Reductants | Key Enzyme |
| Calvin-Benson (N) | Plants, Algae, Cyanobacteria, Aerobic Proteobacteria, Purple bacteria | Light | 3 CO2, 9 ATP,6 NAD(P)H | Glyceraldehyde-3- phosphate | NAD(P)H | RuBisCO |
| rTCA (N) * | Green sulfur bacteria, Proteobacteria, Aquificae, Nitrospirae |
Light and Sulfur |
2 CO2, 2 ATP,4 NAD(P)H |
Pyruvate | NAD(P)H & ferredoxin |
2-Oxoglutarate synthase, Isocitrate dehydrogenase |
| Wood–Ljungdahl (N) * | Acetogenic, Methanogenic Archaea, Planctomycetes, Sulfate. Archaeoglobales, |
Hydrogen | 2 CO2, 1 ATP, 4 NAD(P)H |
Acetyl-CoA | Ferredoxin | NAD-independent formate dehydrogenase, Acetyl-CoA synthase-CO dehydrogenase |
| 3-HP (N) | Chloroflexaceae | Light | 3 HCO, 5 ATP, 5 NAD(P)H | Pyruvate | NAD(P)H | Acetyl-CoA carboxylase, Propionyl-CoA carboxylase |
| HP/HB (N) | Aerobic Sulfolobales | Hydrogen/sulfur | 2 HCO, 4 ATP, 4NAD(P)H | Acetyl-CoA | NAD(P)H | Acetyl-CoA-Propionyl-CoA carboxylase |
| DC/HB (N) * | Anaerobic Thermoproteale,Desulfurococcales | Hydrogen/sulfur | 1 CO2, 1 HCO, 3ATP, 4 NAD(P)H |
Acetyl-CoA | NAD(PH &Ferredoxi |
Pyruvate synthase, PEP carboxylase |
| RHP (CN) | Methanospirillum hungatei | Hydrogen | CO2, 3 ATP, 2 NAD(P)H |
Gluconeogenesis and glycolysis |
NAD(P)H | RuBisCO |
| Natural Reductive Glycine (CD) |
Candidatus phosphitivorax, anaerolimiDesulfovibrio desulfuricans | Phosphite | CO2, ATP, NAD(P), H | Formate/ Pyruvate | NAD(P)H &Ferredoxi |
CO2-reducing formate dehydrogenase(fdhAB) |
| Reverse Otca (CD) | Desulfurella acetivorans | Hydrogen | CO2, ATP, NAD(P) H | Acetyl-CoA | Ferredoxin | Citrate synthase |
| CETCH (S) | Theoretical | – | 2 CO2, 2 ATP, 3 NAD(P)H |
Glyoxylate | NAD(P)H | CoA- dependent carboxylase |
| Reductive Glycine (S) | Demonstrated in E. coli as host | – | CO2, NADH | Pyruvate | Ferredoxin | Glycine cleavage system |
| Synthetic malyl-CoA- glycerate (S) |
Demonstrated in E. coli and Synechococcus elongatus PCC7942 host |
– | CO2, 3 ATP, 3 NADH |
Acetyl-CoA | NAD(P)H | PEP-carboxylase, RuBisCO |
| SACA Pathway (S) | Demonstrated in E. coli as host | – | CO2 | Acetyl-CoA | – | NAD-independent formate dehydrogenase |
| Formolase pathway (S) | Theoretical | – | CO2, NADH, ATP | Dihydroxyacetone- phosphate | NADH | NAD-independent formate dehydrogenase |
Sulamita Santos et al., Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways, Journal of Advanced Research,
Volume 47, 2023, Pages 75-92, ISSN 2090-1232, https://doi.org/10.1016/j.jare. Creative Commons license
Plants and photoautotrophic microorganisms fix CO2 by the Calvin cycle using NADPH and ATP, producing O2. Some anaerobic photosynthetic bacteria don't produce O2. In chemolithoautotrophic microorganisms, energy sources (i.e., electron donors like H2, H2S, sulfur, Fe2+, nitrite, and NH3 found in bedrock - the lithosphere) other than NADPH, ATP, and light can be used to drive CO2 uptake. For chemoorganotrophic microbes, reduced organic molecules such as sugars and amino acids serve as electron (donor) sources.
Genetic engineering and synthetic biology are now employed to improve preexisting enzymes and create new pathways for carbon capture.
As a simple example, people are trying to engineer carbonic anhydrase, which converts CO2 to HCO3-, for transport to the lungs, where it is converted back to CO2 and released. It is a diffusion-controlled enzyme with a kcat/KM reported as high as 8 x 107 M-1s-1, so how can it be made better? One way is to engineer thermal stability into the enzyme. A critical problem for the forward reaction is that the enzyme is readily reversible; thus, bicarbonate, HCO3-, is a competitive inhibitor of the forward reaction. In addition, the enzyme can be engineered to be more stable at higher pH to allow product (HCO3-) removal by the addition of OH- in the process of mineralization, as shown in the equation below,
HCO3- + OH- → CO32- + H2O
where the carbonate anion can precipitate in the presence of divalent cations like Ca2+, Mg2+, and Fe2+. Here is a link to a Literature-based Guided Assessment on thermoengineering of carbonic anhydrase.
Now, let's explore using new pathways created by synthetic biology to capture carbon. Some of these pathways are engineered to produce reactants (feedstocks) for biofuels, which we discussed in depth in Chapter 32, the section on chemical synthesis. We'll focus on the CETCH pathway, the reductive glyoxylate and pyruvate synthesis (rGPS) cycle, and the malyl-CoA-glycerate (MCG) pathway.
CETCH (Crotonyl-CoA-EThylmalonyl-CoA-4Hydorxybutyl-CoA) pathway
To engineer a new pathway, Swander et al identified efficient carboxylases from known ones (acetyl-CoA carboxylase, Rubisco, propionyl-CoA carboxylase, PEP carboxykinase, 2-oxoglutarate carboxylase, and pyruvate carboxylase), all of which we have discussed in previous chapters. They created new pathways, calculated free energy and ATP/NADPH requirements, and optimized the pathways. They chose CoASH–dependent carboxylases and enoyl-CoA carboxylases/reductases. Figure \(\PageIndex{3}\) below shows the reaction of one key carboxylase.
Figure \(\PageIndex{3}\): Carboxylase used in the CETCH pathways to fix CO2
The pathway was named CETCH (Crotonyl-CoA-EThylmalonyl-CoA-4Hydorxybutyl-CoA) which catalyzes this next reaction in cell lysates (in vitro):
2CO2 + 3NAD(P)H + 2ATP + FAD → glycolate + 3NAD(P) + 2ADP +2Pi + FADH2
The rate of CO2 fixation by the CETCH pathways was similar to the rate of the Calvin cycle rates in cell lysates.
In a more expansive approach, Gleizer used synthetic biology to convert E. coli from a heterotroph to an autotroph, with its biomass (carbon reservoir) derived from CO2. Formate (HCO2-) was used as a source of reducing power (electrons), as it was oxidized by an added formate dehydrogenase to produce NADH, which was then used to support the autotrophic fixation of CO2 via the Calvin cycle enzymes. Using isotopically labeled 13CO2 to track carbon flow, after 10 generations of evolution, the cells were completely autotrophic, fixing CO2. To accomplish this, they knocked out genes for phosphofructokinase (glycolysis) and glucose-6-phosphate dehydrogenase (pentose phosphate pathway) to impair these main metabolic pathways. They added carbonic anhydrase (to interconvert CO2 and HCO3-), and Rubisco and phosphoribulokinase. As formate was ultimately converted to CO2, the net effect was not carbon neutral, but could be if atmospheric CO2 was used to make formate (for a feedstock) by electrochemical reduction.
Figure \(\PageIndex{4}\) below shows the next synthetic E. Coli autotroph reactions.
Figure \(\PageIndex{4}\): Schematic Representation of the Engineered Synthetic Chemo-autotrophic E. coli. Shmuel Gleizer et al., Conversion of Escherichia coli to Generate All Biomass Carbon from CO2, Cell, 179 (2019). https://doi.org/10.1016/j.cell.2019.11.009. Creative Commons license.
CO2 (green) is the only carbon source for all the generated biomass. CO2 fixation occurs via an autotrophic carbon assimilation cycle. Formate is oxidized by a recombinant formate dehydrogenase (FDH) to produce CO2 (brown) and NADH. NADH provides the reducing power to drive carbon fixation and serves as the substrate for ATP generation via oxidative phosphorylation (OXPHOS in black). The formate oxidation arrow is thicker than the CO2 fixation arrow, indicating a net CO2 emission even under autotrophic conditions.
Figure \(\PageIndex{5}\) shows that almost 100% of carbon atoms after many generations are labeled with 13C (detected by mass spec analysis) derived from 13CO2.
Figure \(\PageIndex{5}\): Isotopic Labeling Experiments Using 13C Show that All Biomass Components Are Generated from CO2 as the Sole Carbon Source. Gleizer et al., ibid.
(A) Values are based on LC-MS analysis of stable amino acids and sugar-phosphates. The fractional contribution of 13CO2 to various protein-bound amino acids and sugar phosphates in evolved cells grown on 13CO2 and naturally labeled formate was almost complete, indicating full 13C labeling of biosynthesized amino acids. The reported numbers are the 13C fractions of each metabolite, calculated as the effective 13CO2 fraction out of the total inorganic carbon (which decreases due to unlabeled formate oxidation to CO2). The numbers in parentheses are the uncorrected measured values of the 13C fraction of the metabolites.
Synthetic reductive glyoxylate and pyruvate synthesis (rGPS) cycle and the malyl-CoA-glycerate (MCG) pathways
These pathways were created to synthesize acetyl-CoA, pyruvate, and malate from CO2 in cell-free systems, freeing the system from cell growth and regulatory requirements and making it insensitive to oxygen. These molecules are also intermediates in the created cycle, which could operate continuously for hours at the same or greater rates of CO2 fixation compared to photosynthesis. The cycle is shown in Figure \(\PageIndex{6}\) below.
Figure \(\PageIndex{6}\): The rGPS–MCG cycle with acetyl-CoA as the end product. Luo, S., Lin, P.P., Nieh, LY. et al. A cell-free self-replenishing CO2-fixing system. Nat Catal 5, 154–162 (2022). https://doi.org/10.1038/s41929-022-00746-x . Creative Commons Attribution 4.0 International License, http://creativecommons.org/licenses/by/4.0/
The rGPS cycle consists of the reductive glyoxylate synthesis (rGS) pathway (blue) and the reductive pyruvate synthesis (rPS) pathway (green). The malyl-CoA-glycerate (MCG) pathway (orange) consists of the rGS and glycerate pathways. The red arrow indicates the carboxylation reaction. Gcl, glyoxylate carboligase; Tsr, tartronate semialdehyde reductase; Gk, glycerate 2-kinase; Eno, enolase and 2PG, 2-phospho-d-glycerate
Microbial electrosynthesis from CO2
We mentioned above that if the formate used in the CETCH pathway could be synthesized electrochemically from CO2, the pathway would be truly carbon-neutral. New microbial electrochemical methods are being developed to synthesize various small molecules that could serve as feedstocks for industrial chemical synthesis. The carbon in CO2 has an oxidation number of +4, while the carbon in formic acid has an oxidation number of +2. Hence, two electrons must be added electrochemically to make the CETCH pathway truly carbon neutral. Bigger electrochemical reductants of CO2 require more electrons. Figure \(\PageIndex{7}\) below shows how key feedstocks could be made electrochemically from CO2 and how they are usually made in industry.
Figure \(\PageIndex{7}\) : Overview of the Main Products Formed from Microbial Electrosynthesis (MES) From CO2, Along With the Main Industrial Methods to Manufacture These Products. Jourdin et al., Trends in Biotechnology, April 2021, Vol. 39, No. 4 https://doi.org/10.1016/j.tibtech.2020.10.014. Creative Commons Attribution (CC BY 4.0)
These feedstocks could be produced by reductive electrosynthesis using electrons generated by water oxidation via electrolysis. Released electrons (oxidation number of O in water is -2 and 0 in O2) move to a biocathode to reduce CO2, as illustrated in Figure \(\PageIndex{8}\) below.
Figure \(\PageIndex{8}\): Reactor configurations for MES-based CO2 conversion: (a) H-type, (b) single chamber, (c) dual chamber, (d) continuous stirred tank, and (e) schematic of the electron transfer mechanism. G. S. Lekshmi et al., Microbial electrosynthesis: carbonaceous electrode materials for CO2 conversion. Mater. Horiz., 2023, 10, 292-312. DOI: 10.1039/D2MH01178F. Creative Commons Attribution-Non Commercial 3.0 Unported Licence
The biocathode consists of a biofilm of cells printed onto a carbon support (graphene, graphite, or carbon nanotubes).
Marine CO2 Removal Through Geoengineering
As the climate worsens, more climate scientists are considering ways to improve the oceans' ability to capture CO2. Both inorganic and biological methods have been proposed. These methods will likely have unintended consequences, affecting biodiversity and the natural mechanisms for carbon sequestration. Hence, they are both controversial.
Inorganic:
Here is a review from Chapter 32.3: The Carbon Cycle and Carbon Chemistry
The reversible movement of CO2 from the atmosphere to the oceans, CO2 atm ↔ CO2 ocean, depends on the difference in the partial pressures of CO2 (ΔpCO2) in the atmosphere and surface waters. The reaction is also driven to the right by the removal of CO2 (aq) as it forms carbonic acid (H2CO3), which then forms bicarbonate (HCO3–) and carbonate (CO32–). These coupled reactions chemically buffer ocean water, thus regulating ocean pCO2 and pH.
pCO2 is not homogeneous in ocean surface waters and varies with current and temperature conditions. CO2 can be more readily released from upwellings of nutrient-rich and warm waters, especially in the tropics. In cold Northern waters and the Southern Ocean, where water sinks, it is taken up from the atmosphere (again, CO2 is more soluble in cold water).
As we discussed in Chapter 31.1, ocean chemistry of CO2 largely determines atmospheric CO2 levels. The coupled reactions of CO2 in the oceans are shown below.
\begin{equation}
\mathrm{CO}_2(\mathrm{~g}, \mathrm{~atm}) \leftrightarrow \mathrm{CO}_2(\mathrm{aq}, \text { ocean) }
\end{equation}
\begin{equation}
\mathrm{CO}_2(\mathrm{aq} \text {, ocean })+\mathrm{H}_2 \mathrm{O}(\mathrm{I} \text {, ocean }) \leftrightarrow \mathrm{H}_3 \mathrm{O}^{+}(\mathrm{aq})+\mathrm{HCO}_3^{-}(\mathrm{aq})
\end{equation}
\begin{equation}
\mathrm{H}_2 \mathrm{O}(\mathrm{I})+\mathrm{HCO}_3^{-}(\mathrm{aq}) \leftrightarrow \mathrm{H}_3 \mathrm{O}^{+}(\mathrm{aq})+\mathrm{CO}_3{ }^{2-}(\mathrm{aq} \text {, sparingly soluble })
\end{equation}
These reactions should be familiar to all chemistry students and were presented previously in Chapter 31.1 and Chapter 2. A significant source of oceanic bicarbonate is the weathering of rocks such as limestone and marble, both forms of CaCO3. The relevant reactions are shown below.
\begin{equation}
\begin{aligned}
&\mathrm{CaCO}_3(\mathrm{~s})+\mathrm{H}_2 \mathrm{O} \leftrightarrow \mathrm{Ca}^{2+}(\mathrm{aq})+\mathrm{CO}_3{ }^{2-}(\mathrm{aq}) \\
&\mathrm{CO}_3{ }^{2-}(\mathrm{aq})+\mathrm{H}_2 \mathrm{O} \leftrightarrow \mathrm{HCO}_3{ }^{-}(\mathrm{aq})+\mathrm{OH}^{-}(\mathrm{aq})
\end{aligned}
\end{equation}
CO2 is nonpolar and not very soluble in water. Either is CO32- in the presence of divalent cations like Ca2+. However, HCO3- is and can be considered a "soluble" form of carbon. This soluble form from terrestrial weathering enters rivers and eventually reaches the ocean. It is also the form of carbonate that is transferred into cells by anion transporters for eventual shell formation. HCO3- is also a chief regulator of both blood and ocean pH. Weathering is slow compared to anthropogenic CO2 emissions from fossil fuel use, but it is nevertheless a key player in the carbon cycle and in regulating ocean pH.
The same weathering reactions on silicate rocks release silicate ions into rivers and the ocean, where they can be used by diatoms to form CaSiO4 shells. As the oceans take up more CO2, they become more acidic, mimicking "weathering" of the shells of living organisms and potentially leading to their death. Silicon is directly underneath carbon in the periodic table, so this simplified reaction is analogous to those we see with CO2 and its inorganic ions.
\begin{equation}
\mathrm{H}_4 \mathrm{SiO}_4=\mathrm{SiO}_2+2 \mathrm{H}_2 \mathrm{O}
\end{equation}
H4SiO4 is silicic acid.
With this background in mind, you can understand the proposed method of adding crushed limestone (CaCO3) to the rivers (which drain into the oceans) to remove atmospheric CO2. As the solid crushed limestone dilutes, it becomes more soluble. As CO32- is a reasonable base, the water would become more alkaline. It would mostly get converted to HCO3- which can be transported into river shell-forming organisms. The rest enters the oceans, where it can be transported into organisms and used to make CaCO3 shells, eventually sinking to the depths where the carbon would be sequestered for 1000s of years. This would also reduce river acidification. Whether this process could be run at the scale needed to reduce atmospheric CO2 significantly is unclear.
Biological
This method involves adding Fe2+, usually iron (II) sulfate (FeSO4), to the oceans to promote phytoplankton growth. This process has been called ocean iron fertilization (OIF). One problem with FeSO4 is that it rapidly oxidizes to insoluble iron(III) species at elevated temperatures. It must be transported to sufficient depths so it doesn't return to the surface. Another problem is the adverse effects of nutrient removal on other marine organisms.
Summary
(Summary written by Claude, Anthropic)
Carbon fixation — converting atmospheric CO₂ into organic biomolecules — removes approximately 100 petagrams of carbon per year through net primary production, split roughly equally between land and ocean organisms. The dominant enzyme is RuBisCO, which despite its global importance is remarkably slow (kcat ≈ 2–10 CO₂/sec), requires a chaperonin for assembly, and is compromised by a competing oxygenase reaction that drives wasteful photorespiration. While planting trees is widely proposed as a climate solution, old-growth forests are far more effective carbon sinks than new plantings, which require decades before contributing meaningfully to drawdown. The chapter therefore focuses on engineering improved and entirely new carbon fixation strategies.
Natural carbon fixation pathways. Six naturally occurring pathways fix CO₂ beyond the Calvin-Benson-Bassham (CBB) cycle. The reverse TCA cycle fixes CO₂ into pyruvate in green sulfur bacteria using ferredoxin and NAD(P)H. The Wood–Ljungdahl pathway, used by acetogenic and methanogenic Archaea, is one of the most energy-efficient routes, producing acetyl-CoA from two CO₂ molecules using hydrogen as the energy source. The 3-hydroxypropionate cycle (Chloroflexaceae) uses acetyl-CoA and propionyl-CoA carboxylases to fix bicarbonate. The HP/HB and DC/HB cycles (thermophilic Archaea) use hydrogen and sulfur to produce acetyl-CoA under anaerobic conditions. These pathways collectively demonstrate the metabolic diversity available for CO₂ capture and provide a toolkit for synthetic biology.
Engineered carbonic anhydrase. As an entry point to synthetic carbon capture, carbonic anhydrase — which interconverts CO₂ and HCO₃⁻ at near-diffusion-controlled rates (kcat/KM up to 8 × 10⁷ M⁻¹s⁻¹) — is being engineered for greater thermal stability and higher pH tolerance. The key challenge is product inhibition: HCO₃⁻ competitively inhibits the forward reaction. Engineering the enzyme to function at higher pH allows OH⁻ addition to drive HCO₃⁻ to CO₃²⁻, which precipitates with Ca²⁺, Mg²⁺, or Fe²⁺ as insoluble carbonate minerals — permanently sequestering the captured carbon.
Synthetic carbon fixation pathways. The CETCH pathway (Crotonyl-CoA/EThylmalonyl-CoA/4-Hydroxybutyryl-CoA) was designed computationally by selecting efficient CoA-dependent carboxylases and enoyl-CoA carboxylases/reductases from known enzymes and optimizing the pathway for thermodynamic feasibility and cofactor balance. Operating in cell lysates, it fixes 2 CO₂ per cycle to produce glyoxylate: 2CO₂ + 3NAD(P)H + 2ATP + FAD → glycolate + cofactors, at rates comparable to the Calvin cycle in vitro. In a more ambitious approach, Gleizer et al. converted E. coli from a heterotroph into a fully autotrophic organism by knocking out phosphofructokinase and glucose-6-phosphate dehydrogenase (disabling glycolysis and the pentose phosphate pathway), and adding RuBisCO, phosphoribulokinase, and carbonic anhydrase. Formate served as the electron donor, oxidized by formate dehydrogenase to generate NADH for CO₂ fixation. After directed evolution over 10 generations, ¹³CO₂ isotopic labeling confirmed that virtually 100% of cellular carbon derived from CO₂. The rGPS–MCG cell-free pathway (reductive glyoxylate/pyruvate synthesis + malyl-CoA-glycerate) takes this further by operating entirely outside living cells — avoiding regulatory constraints, oxygen sensitivity, and competition with cellular metabolism — while fixing CO₂ into acetyl-CoA, pyruvate, and malate at rates matching or exceeding photosynthesis continuously for hours.
Microbial electrosynthesis. To make pathways like CETCH truly carbon-neutral, formate feedstocks must themselves be produced from atmospheric CO₂. Microbial electrosynthesis (MES) achieves this by delivering electrons from water electrolysis to a biocathode — a biofilm of microorganisms on graphene, graphite, or carbon nanotube supports — where CO₂ is reduced. Converting CO₂ (+4 oxidation state) to formate (+2) requires two electrons; larger products require more. This electrochemical approach, powered by renewable electricity, could close the carbon loop for synthetic fixation pathways.
Marine CO₂ removal by geoengineering. As biological and synthetic approaches develop, ocean-based geoengineering is also being explored, though both proposed approaches are controversial due to potential unintended ecological consequences. The inorganic approach (ocean alkalinity enhancement) involves adding crushed limestone (CaCO₃) to rivers; as it dissolves, it raises water alkalinity, converting CO₂ to HCO₃⁻, which eventually enters marine organisms as shell material (CaCO₃), sinks to the ocean floor, and sequesters carbon for thousands of years — also mitigating river and coastal acidification. Whether this is scalable to climatically meaningful levels remains uncertain. The biological approach — ocean iron fertilization (OIF) — adds FeSO₄ to iron-limited surface waters to stimulate phytoplankton blooms and biological CO₂ uptake. Practical challenges include rapid oxidation of Fe²⁺ to insoluble Fe³⁺ at the surface, the need to deliver iron to depth, and disruption of marine nutrient cycles and biodiversity.
Throughout, the chapter emphasizes that all carbon capture strategies complement but cannot substitute for the primary imperative: drastically reducing fossil fuel combustion.


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