CONTRIBUTION

Wet Lab

  • We created cosmobiome, a novel closed-loop co-culture of silicate-solubilizing bacteria and diatoms for in situ resource utilization and biomanufacturing on Mars.

  • This is the first iGEM project that makes use of silicon compounds present in the Martian regolith in order to drive a biological process.

  • Through our experimental work, we designed and implemented various novel protocols and procedures. Some of these include:

  • Extending an existing protocol to use liquid media to screen silicate solubilizers for any choice of silicate compound

  • Creating a novel protocol for researchers and future iGEM teams to handle Martian soil simulants and culture bacteria in them

  • Testing bacterial growth in soil at different salinities for optimization of co-culturing with more halotolerant species

  • Defining a co-culture protocol for growing bacteria and diatoms together

  • As a proof-of-concept, we demonstrated how our co-culture system can be used to manufacture limonene, a useful platform chemical, on Mars. We also demonstrated how our system is compatible with iGEM BioBricks.

  • We also provided an idea for scaling up space synthetic biology projects from the lab-scale to a bioreactor on Mars. We also created a framework for the systematic analysis of the efficacy of synthetic biology-based ISRU projects by analyzing our own co-culture system.

Model

We demonstrated 3 distinct and detailed modeling approaches to qualitatively and quantitatively simulate our space synthetic biology project. These strategies can be employed by other teams when they are performing their own modeling tasks.

  • Our constraint-based genome scale metabolic modeling creates a workflow for the analysis of metabolic systems and to optimize the production of target metabolites, which can also be engineered into the system.

  • Our analysis also involved employing the FSEOF algorithm for the first time to a plant / algal system. This revealed gene overexpression targets to maximize product yield.

  • We demonstrated Escher plots of a genome-scale metabolic model (GSMM) for an organism outside of Escherichia coli and Saccharomyces cerevisiae for the first time. Our approach to creating these can be used by others in the systems biology community to obtain valuable visual insights from their own genome scale metabolic modeling.

  • We developed a novel dynamic model to represent the process of silicate solubilization. This process is crucial, as crystalline silicates have limited utility compared to their solubilized form. Although obtaining quantitative results was challenging due to insufficient available data, we were able to qualitatively demonstrate that the model aligns with findings from the literature and wet lab experiments. This work represents a significant step toward creating a comprehensive model that fully integrates all aspects of silicate solubilization.

  • We constructed a novel community model using MICOM that, for the first time, incorporates silica as a metabolite. This serves as a foundational step toward developing future models that integrate additional inorganic molecules. Our MICOM model successfully produced results consistent with wet lab findings. 

  • This was also the first time the MICOM framework was used to model a two species co-culture of a prokaryotic and eukaryotic species.

Software

  • As a result of the difficulties we faced when ideating for a problem statement to tackle ISRU, we have created Astrolabe. This is a software tool that recommends chassis organisms based on the  resources available and environmental conditions of a host planet or celestial body.

  • We believe this is the first ever chassis recommendation algorithm and the first ever software tool for space synthetic biology.

  • Astrolabe will enable researchers around the world to develop new synthetic biological approaches to in situ resource utilization and space biomanufacturing.

  • It also has broader applications wherever chassis selection is crucial.

  • The software includes support for minerals, organics and gases, allowing the consideration of various celestial bodies including terrestrial and gaseous planets and moons in and beyond the solar system. 

  • Our software integrates various bioinformatics databases including UniProt, BioCyc, KEGG, BRENDA, BacDive and MediaDive. 

  • In addition, we also present a web tool for Astrolabe, which offers a GUI frontend and allows for easy trial of the software.