I am an architect pursuing bio-integrated design at The Bartlett School of Architecture.
See the nav bar on the left to look through my work for How To Biomanufacture Almost Anything (Fall 2026)!
1. WHAT and WHY?
The idea is to create a site-specific tubular artifact/installation that captures methane from the landfills and biomanufactures Polyhydroxybutyrate (PHB), a bio-degradable polymer.
The project explores how waste sites can also act as sites for biomanufacturing. Landfills generate methane through decomposition of organic waste. This locally available carbon source can be continuously used as the feedstock for biological processes.
The proposed artefact would have a dual role, a bio-reactor and visual interface for people to interact with. Methanotrophic bacteria would consume methane to accumulate PHB in their cells, under specific conditions. In a given cycle, a fixed amount of methane enters the system, less methane present in the tubes would signal more PHB production. The proposed site-specific installation would sense the methane concentrations in the tubes and create different intensities of light.
Less Methane consumed (less PHB production), less intense lights
More Methane consumed (High PHB production), more intense lights
The lighting system will provide visibility to the bio-manufacturing process allowing people to interact with the installation.
2. LIVING SYSTEMS
The proposed chassis is a PHB-producing Methanotrophic Bacteria (Methylocystis sp.).
The project aims to use DNA circuit design to optimise PHB production when a certain Biomass threshold is achieved. The internal surface area of the tubular system would determine the microbial growth and define the biomass threshold at which the system goes from growth to production mode. This programmable system would create a balance between microbial growth and material production.
3. AUTOMATION
The project presents a two-fold automation strategy.
A.DNA circuit design to provide a growth vs production switch (environmental control and sensing, sampling)
B.Lighting control through Methane sensing to make biomanufacturing interactive
For these strategies, an automated bioreactor with a sensor + actuator system is proposed.
The automated sensing technology would handle methane sensing and biomass monitoring. The inlet valves will be programmed based on this data. The environmental control within the bioreactor would also be monitored to keep track of nutrient levels, oxygen, pH and temperature. Periodic samples would be removed and assessed for PHB production.
The methane sensing system would control the light intensity in different parts of the tubes.
4. SCALE
For the initial prototype, the target is to biomanufacture around 500g of PHB. This would provide proof of concept for scaling up the idea.
A recent study by Hong et al. (2025) achieved 34.5 g/L of PHB content after 162 hours of cultivation. Using this as a starting point,
Volume of culture: 500g / 34.5 g/L = 14.49 L of culture
A 20 L bioreactor is proposed as a demonstrator.
Estimated time: 34.5 g/L / 160 h * 20L = 4.26 g/h
500 g / 4.26 g/H = 117.4 h
5. UNKNOWNS
A. Can engineered Methylocystis bacteria switch from growth to production mode? B. Can methane from landfills be a reliable source? C. Can this system be scaled-up to achieve high PBH productivity?
References
Hong, H. J., Hyung, J. S., Lee, J., & Na, J.-G. (2024). Effects of methane to oxygen ratio on cell growth and polyhydroxybutyrate synthesis in high cell density cultivation of Methylocystis sp. MJC1. Environmental Science and Pollution Research, 32(28), 16715–16724. https://doi.org/10.1007/s11356-024-33524-2
Naizabekov, S., Hyun, S. W., Na, J.-G., Yoon, S., Lee, O. K., & Lee, E. Y. (2023). Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis. PLOS ONE, 18(5), e0284846. https://doi.org/10.1371/journal.pone.0284846
Safaeian, P., Yazdian, F., Khosravi-Darani, K., Rashedi, H., & Lackner, M. (2023). P3HB from CH4 using methanotrophs: Aspects of bioreactor, fermentation process and modelling for cost-effective biopolymer production. Frontiers in Bioengineering and Biotechnology, 11. https://doi.org/10.3389/fbioe.2023.1137749
Taskan, B., Taskan, E., Lai, Y. S., Eustance, E., Mahmood, M., Luo, Y., & Rittmann, B. E. (2025). Polyhydroxybutyrate (Phb) production and methane uptake by methanotrophic bacteria in a membrane-based reactor. Chemosphere, 385, 144590. https://doi.org/10.1016/j.chemosphere.2025.144590
AI use statement: ChatGPT (OpenAI, GPT-5.6 Luna) was used during the development of this proposal to support language editing, and back-of-the-envelope calculations. Scientific claims and cited sources were independently reviewed and verified by the author.
1. What molecule are you expressing?
The target product is polyhydroxybutyrate (PHB), a biodegradable polymer. Because PHB is a material rather than a single protein, the genetic construct is designed to express the three enzymes of the PHB biosynthesis pathway:
PhaA — acetyl-CoA acetyltransferase PhaB — acetoacetyl-CoA reductase PhaC — PHB synthase
Together, these enzymes convert acetyl-CoA into PHB. The three-enzyme pathway is also associated with PHB production in Methylocystis and other PHB-producing bacteria.
2. What is the sequence?
The construct encodes the phaA, phaB and phaC coding sequences. For the initial design, the sequences are taken from known database/BioBrick parts available in Kernel, rather than designed de novo.
The selected PhaA sequence is from Cupriavidus necator and is an unmodified coding sequence for acetyl-CoA acetyltransferase. The PhaB and PhaC sequences are also selected as known PHB-pathway parts from the Kernel library.
Because these genes originate from organisms other than the final Methylocystis chassis, the CDSs will subsequently be codon-optimized for the host as part of Part 4.
3. What host or chassis?
The proposed chassis is a PHB-producing Methylocystis sp. methanotroph.
Methylocystis is a Type II methanotroph capable of using methane as a carbon and energy source, and members of the genus naturally produce PHB. For example, Methylocystis sp. MJC1 has demonstrated substantial PHB production from methane.
The host is therefore important to the design because the promoter, RBS, codon usage and other expression elements need to be compatible with a bacterial Methylocystis chassis.
4. Where does the product need to go?
Cytoplasm / intracellular accumulation.
PHB is accumulated inside the bacterial cells as intracellular polymer granules, rather than being secreted outside the cell. Therefore, the construct does not require a signal peptide or secretion sequence.
The PHB will subsequently need to be recovered from the biomass as part of the downstream process; the genetic construct itself is designed for intracellular PHB production.
CODON OPTIMISATION
The selected Methylocystis chassis was not available as a codon-optimization target in Kernel. Therefore, a host-specific optimization could not be directly performed. The CDSs were retained as the starting sequences, and optimization for a closely related methanotroph would be considered in a future design iteration.