Carbon capture and utilisation to replace sugar-based fermentations in the biotechnology industry

Industrial biotechnology relies on agriculture to provide the input energy in the form of sugars for bacterial fermentations. Sugars are the carbon source and the energy source in these traditional setups. However, certain bacterial species are able to utilise carbon dioxide as their carbon source while relying on hydrogen gas as their energy source; these species are Hydrogen Oxidising Bacteria (HOB).

The biochemical route exercised in HOB is the most efficient form of biological carbon fixation including photosynthetic algae.

Several companies are attempting to commercialise the use of HOB to make Single Cell Protein (SCP), which is sold as a proteinaceous feed ingredient. As a feed ingredient SCP has major environmental advantages over traditional feed proteins: it has a lower overall carbon footprint in addition to a dramatically lower land and water use. However, for full uptake of the technology commercially the product must have sufficiently high value to compensate for the input costs and relatively high capital costs of a commercial plant.

Adoption of this technology benefits from the ramp up in interest and scaling of the hydrogen economy.

One particularly attractive route for improving the value of SCP is to co-produce other biological compounds of commercial interest such as dyes, flavourings, fragrances, or antioxidants. If these can be produced by the bacteria and extracted during downstream processing then the economics of SCP as a feed ingredient may become significantly more favourable.

In the long-term the HOB will be engineered to compete technically with established species which currently make higher value compounds, but the HOB will have the advantage of using a hydrogen and carbon dioxide input stream rather than a sugar-based input.

Established strains in industrial biotechnology are highly adapted or engineered to maximise productivity. HOB have not been the target of these manipulations historically because of a lack of inherent predisposition as a production organism. However, the ability to grow on a mixture of carbon dioxide and hydrogen is a highly desirable trait because of the environmental benefits of this process compared to one dependent on agricultural products as an input stream.

In addition, this ability is not one that can be easily transferred to the established production strains. A far simpler approach would be to transfer the relevant properties from the established production strains to the HOB.

Deep Branch has a library of HOB capable of growing on carbon dioxide. Within that library there are several strains for which a genetic toolkit has been developed which allows sophisticated genetic engineering to be performed.

Escherichia coli is the most widely used species for expressing high value proteins largely because of the genetic toolkit which has been developed for it. This project aims firstly to emulate many of the developments which have made E. coli the dominant species in industrial biotechnology primarily by engineering strong protein expression systems comprising promoters, ribosome binding sites, and powerful dedicated RNA polymerases.

Certain bacterial species are naturally well evolved to produce a given class of biological compound for instance an antibiotic. Other species would have evolved in such a way as to make them ideal candidates for the production of chemically dissimilar compounds such as dyes or flavours. To assess the suitability of the chosen HOB for the production of different classes of compounds a range of compounds will be chosen for expression.

This will help to inform the most appropriate target for optimisation and deployment in a commercial setting.

Another goal will be to increase the efficiency of carbon capture via protein engineering. This will involve identifying the bottleneck in the biochemical pathway of carbon fixation and making a library of different versions of the bottleneck protein.