27.02.2025 Synthetic Carbon Assimilation Surpasses Nature

New-to-Nature Pathway Outperforms Natural Pathway in Living Bacteria

A bioreactor experiment showed that the non-phototrophic bacterium Cupriavidus necator can produce more biomass with a synthetic metabolic pathway from formic acid and CO2 than the natural bacterial strain. To the left, Dr. Beau Dronsella.

For the first time, an international collaboration has demonstrated that synthetic carbon assimilation can operate more efficiently in a living system than its natural counterpart. Researchers in Tobias Erb’s lab at the Max Planck Institute for Terrestrial Microbiology engineered a synthetic metabolic pathway into a bacterium and showed in a direct comparison that it can generate significantly more biomass from the one-carbon compound formic acid and CO₂ than the natural bacterial strain. The researchers report on their findings in recent issue of Nature Microbiology (Feb 27, 2025).

In nature, CO₂ is primarily fixed through the Calvin cycle, which is part of photosynthesis. However, this natural fixation pathway has efficiency limitations. Tobias Erb, director at MPI and full professor at Marburg University, and his team have previously developed artificial cycles such as the CETCH and THETA cycles, which outperform the natural Calvin cycle in efficiency. These pathways have already been successful in test tubes but have only been partially integrated into living organisms.

Another approach to CO₂ fixation under active research involves physical-chemical methods, such as the electrochemical reduction of CO₂ into formic acid using renewable energy. However, these methods struggle with further processing formic acid into complex molecules like sugars or proteins. Some bacteria, on the other hand, can grow on formic acid and make various products. Therefore, researchers are currently developing hybrid techniques that first fix CO₂ physically-chemically into formic acid and then further process it microbially.

Sustainable Hybrid Solutions 

Since many bacteria naturally convert formic acid through the Calvin cycle, synthetic alternatives like CETCH could be used to make the microbial part of the hybrid process more productive and generate desired raw materials more sustainably. But are these synthetic, human-designed carbon-processing pathways truly more efficient than natural ones in direct comparison?

To answer this question, the research team tested the "reductive glycine pathway," as it is the most efficient synthetic metabolic route for processing formic acid. To prove that it could energetically outperform natural carbon fixation via the Calvin cycle, they selected the non-phototrophic bacterium Cupriavidus necator, which naturally uses the Calvin cycle to metabolize formic acid. In 2020, one of the team’s collaborators, Dr. Nico Claassens from Wageningen University, had already successfully introduced the reductive glycine pathway into this organism. However, the resulting growth rates and biomass yield—key indicators of metabolic efficiency—were lower than those of the unmodified bacterium.

Optimization via Laboratory Evolution 

In the new study, the researchers transplanted the complete reductive glycine pathway into the bacterium’s genome, this time optimizing its efficiency. They used mobile DNA elements capable of randomly integrating into the genome and loaded them with components of the reductive glycine pathway. By optimizing genomic modifications through laboratory evolution for growth on formic acid, they enhanced the pathway’s efficiency. "Cells in which the genes of the reductive glycine pathway were favorably integrated and expressed grew better than others and were selectively enriched until their production was close to the physiological optimum," explains Dr. Beau Dronsella, the study’s first author, published in Nature Microbiology.

Head to Head: Synthetic versus Natural 

The artificially modified and optimized strain was able to produce significantly more biomass from formic acid and CO₂ than the natural bacterial strain. The researchers even measured higher biomass yields than any previously recorded formic acid-based biomass production by organisms using either the Calvin cycle or synthetic pathways. However, the artificially modified strain was only half as fast as the natural one.

Potential for future bioproduction

The researchers remain optimistic that adaptive laboratory evolution can further close this gap. The proof that synthetic biology can indeed be used more efficiently in a biotechnological setting to fix carbon is not just relevant for the reductive glycine pathway but for many artificial metabolic routes under development. "Our findings hold great potential for sustainable bioproduction from formic acid and could also enhance existing bioproduction processes," says Beau Dronsella. "Ultimately, formic acid—similar to hydrogen—could serve as a chemical energy carrier, allowing renewable energy surpluses to be stored and used for bioproduction in the future." For Tobias Erb, this study marks a significant milestone in the emerging field of synthetic biology: "It is fascinating that, with synthetic biology, we can design new solutions within a few years that outperform what has evolved in nature over billions of years."

Original Publication: Dronsella, B.; Orsi, E.; Schulz-Mirbach, H.; Benito-Vaquerizo, S.; Yilmaz, S.; Glatter, T.; Bar-Even, A.;. Erb, T.J.E.;  Claassens, N. J., One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle, Nature Microbiology Feb 27 (2025), DOI: 10.1038/s41564-025-01941-9

Source: Press release of the MPI or Terrestrial Microbiology, Marburg.