Biocementing Bacteria

This page outlines the development of engineered microorganisms capable of microbially induced calcite precipitation (MICP) through surface-displayed carbonic anhydrase. By combining enzyme optimization, chassis selection, and surface localization strategies, we aim to create bacteria that can convert atmospheric CO₂ into stable calcium carbonate for sustainable biocementation on Earth and Mars.

E. coli

To evaluate and compare surface display efficiency across species, E. coli was used as a benchmark chassis alongside Caulobacter crescentus and Synechococcus elongatus UTEX 2973. Using an established construct design from the distribution kit, we performed transformations and validation experiments to assess expression and functionality of the surface display system under standardized conditions.

Functional Validation

This page outlines the experimental framework for validating surface-displayed carbonic anhydrase (CA) constructs across E. coli, Caulobacter crescentus, and Synechococcus elongatus UTEX. It connects molecular-level validation, protein localization and enzymatic activity, with biomineralization, establishing a full workflow from expression to microbially induced calcium carbonate precipitation (MICP).

Modelling

To assist Wet Lab in selecting candidates for surface display, AlphaFold was used to generate 3D models of the fusion proteins. Structural alignment on PyMOL allowed for the investigation of conformational changes. Finally, the stability of the proteins were analyzed through molecular dynamics simulations with GROMACS.

Parts

To help other teams to create their own surface-displaying bacteria, we have created and submitted several parts to the iGEM Registry. Check them out here!

Lab Notebook: Biocementing Bacteria

Bioreactor Overview

An iGEM classic, bioreactors are crucial to synthetic biology projects, providing and optimizing bacterial growth to increase wet lab stock and decreasing costs. This year, we built two bioreactors tailored towards our two chassis, C. crescentus and S. Elongatus. Our research questions for these two bioreactors explores the characteristics of each and how they affect our bioreactors’ conditions.

CB2A Bioreactor: Build

The build process for CB2A Bioreactor involved implementing designs that met our requirements outlined in the previous page. We primarily used polylactic acid (PLA) to manufacture custom parts and used an Arduino to test the first few iterations. We also performed simulations in SolidWorks to explore shear stresses in silico.

CB2A Bioreactor: Validation

To validate the CB2A bioreactor, we ran growth curves in our bioreactor and compared it to traditional methods that used culture flasks and shakers. We used the 30 °C temperature-controlled room and sampled using optical density at 600 nm at a frequency of 1 hour. Ultimately, we found that we were able to reach exponential phase quicker than wet lab, but heating issues stunted the curve later.

UTEX 2973 Bioreactor: Media Optimization

To maximize the growth of UTEX 2973 in our bioreactors for optimal production of living building materials, we implemented flux balance analysis modelling to determine what the optimal BG-11 media composition and culture conditions are that maximizes UTEX 2973 growth rate.

Low-Gravity Bioreactor: Build

Building the low gravity simulator presented a unique challenge in the importance of symmetry and dynamic movement. We ran into slight issues when 3D printed parts were slightly asymmetrical, causing imperfect revolution building mechanical stress into the structure. We included bearings and slip rings to counteract wire tangling and ensuring smooth rotation.

Low-Gravity Bioreactor: Validation

Validation for our low gravity simulator was particularly tricky because it was difficult to find a way where we could get unbiased quantitative data from the interior of the vessel during operation. Using literature, we adapted some qualitative tests that can indicate that low gravity may be present within the vessel.

Bioprinter: Overview

We modified a 3D clay printer into a bioprinter compatible with our novel bioink. We created a biomaterial composition that can incorporate microbes to serve as a bioink for bioprinting 3D living building materials for Mars.

Bioink: Calcium Diffusion Modelling

This page details the computational approach for simulating diffusion and crosslinking processes in alginate-based ink formulations.

Bioprinter: Requirements + Design

This adapted bioprinter will be used to test and characterise the bioink produced for meduCA. In this page, we’ll outline the modifications and requirements we need to sufficiently meet these goals. We used a TronXY Moore 1 and modified it with a syringe pump for extrusion and added a holder for bioink.

Bioprinter: Validation

Validating the bioprinter involved the completed and optimized bioink to produce basic geometric structures and testing their strengths. We will be testing its capabilities by printing at slow speeds in 2D and 3D squares, comparing the results to experiments conducted by the bioink team as a control.

Lab Notebook: Bioprinter & Bioink

Lab notebook entries related to developing the bioink and bioprinter.

Software

Innovative software tools that power meduCA and accelerate breakthroughs in synthetic biology.

maestro

A task orchestration framework for reproducible, distributable bioinformatic workflows.

miso

A framework to develop intuitive user interfaces for meduCA’s bioreactors and the next generation of hardware in iGEM.

Education

The Education subteam focuses on delivering synthetic biology programming and fostering community awareness through impact-driven initiatives. Learn more about how we developed our educational curriculum in this page!

Synthetic Biology Children’s Storybook

The Synthetic Biology Children’s Storybook engages young readers with space exploration and scientific research. Learn more about how we designed our storybook in this page!

Inclusivity

We ask all those who work or have worked in a wet lab; what would your life look like if something happened to your hands?

Iterative DBTL Cycles

This step in our design process begins our 3D modelling and printing stage. Prototypes were welcomed, such as custom clay molds to better understand our user’s comfort and quantify thicknesses. Many DBTL cycles were required to reach a viable product.

Project Outcomes

During our final meeting with our user, we provided her with the add on that now perfectly fit her pipette and qualitatively evaluated her comfort and level of upper-limb strain with and without the pipette. We saw a visible reduction in her use of her wrist tendons, and to quantify this value, we conducted tests with EMG electrodes. Despite having limitations such as a lack of pipette knob support, non-squishy material and a smooth surface (our user prefers a textured pipette to increase her grip), this add on was able to reduce our user’s hand intensity when handling her pipette while also being lightweight and sterilizable, all of which make it a helpful tool that can be further iterated to make optimal to many individuals that have upper-limb musculoskeletal disorders.

Best Practices for Inclusive Design Project

The Inclusive Lab Space is an intended framework for the iGEM community to conduct their own inclusive design projects. Walk through our design process and learn about areas where our team performed or diverged from the best practices, and how to approach challenging aspects of an inclusive design project.

Needs Finding

What commercializable issue is currently unresolved in the market, and who would want such a solution?

Strategic Planning

What is our core business model and how can we grow our business in terms of customers and funding?

Long Term Growth

What is the ultimate goal of the business? What long-term plans do we have for the business, and its impacts on society?

Medal Criteria

To help demonstrate our team’s achievements to the judges, we put together a judging summary page to guide you to each deliverable!

Human Practices

Our Human Practices page displays all expert & stakeholder interviews which helped drive meduCA forward across our deliverables!

Attributions

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Awards

shiny medal :)