Abstract
Cement production cement-based construction materials like concrete and bricks are responsible for around 8% of global anthropogenic CO₂ emissions (Kajaste & Hurme, 2016). Multiple factors will lead to rising demand for cement in the coming decades and thereby increase the output of CO₂ from this sector (Castro-Alonso et al., 2019; Lanjewar et al., 2025). At Pyricon, we are tackling this environmental challenge head-on by designing a sustainable, bio-based alternative to cement bricks. We engineer Bacillus subtilis to produce spider silk proteins to enhance microbially induced calcite precipitation by another bacterium, forming a sustainable biocement. Using a novel, PCR-free DNA assembly strategy and codon harmonisation, we overcome challenges in constructing and expressing highly repetitive silk genes. Our project not only enables eco-friendly construction materials but also introduces a versatile method for assembling complex synthetic DNA sequences. If adopted at scale, Pyricon’s bio-cement approach could substantially reduce embodied CO₂ in masonry and small-scale construction while simultaneously extending service life, offering a practical pathway toward lower-carbon built environments.
Our Motivation
Climate change poses an unprecedented threat to society and the global economy. The latest Intergovernmental Panel on Climate Change (IPCC) report warns that the world is on track to far exceed the 1.5 °C target (Lee et al., 2023). CO₂ emissions are a key driver of global warming and continue to rise, with high-emission sectors like construction playing a particularly significant role. Cement and concrete production alone account for approximately 8% of anthropogenic CO₂ emissions (Kajaste & Hurme, 2016). In 2024, cement production contributed an estimated 1.5 gigatons of CO₂ (Copernicus Climate Change Service [C3S], 2024).
As populations grow and urbanization expands, demand for cement and concrete is only increasing. Concrete is already the second most consumed material on Earth after water (Achal & Mukherjee, 2015; Farfan et al., 2019). At the same time, concrete structures face durability issues. Over decades, they crack due to mechanical stress, freeze–thaw cycles, or chemical corrosion. These cracks reduce integrity and allow water ingress, further accelerating degradation (Castro-Alonso et al., 2019). Repairing them requires additional cement, compounding emissions. Reducing its climate impact is therefore a pressing priority for sustainable development.
Volumetric visualization of the total carbon dioxide (CO₂) on a global scale added on Earth's atmosphere over the course of the year 2021. Credits: NASA's Scientific Visualization Studio.
The Problem
The process requires heating limestone to ~1450 °C, an energy-intensive step that contributes ~30% of emissions (Semugaza et al., 2023). More critically, ~60% of emissions come from the calcination reaction itself, which chemically releases CO₂ as limestone decomposes (Gjorv & Sakai, 1999; He et al., 2019). These emissions cannot be solved by switching to renewable energy or improving efficiency, they are intrinsic to the material.
A wide range of technical and industrial strategies exist to reduce the carbon footprint of cement and concrete. Many large manufacturers focus first on operational and circular measures, for example increasing the share of alternative fuels, improving kiln efficiency, using recycled concrete and aggregates, and producing blended cements with lower clinker content. Companies such as Heidelberg Materials promote composite and lower-clinker products and highlight recycling and circularity initiatives as primary levers for reducing emissions. These approaches can reduce emissions on a per-tonne basis and are attractive because they fit within existing production and supply chains. However, most do not eliminate the fundamental chemical CO₂ released by limestone calcination, which remains a large fraction of total process emissions.
Our Solution
We aim to address both the CO₂ emissions of cement production and the structural degradation of concrete by developing a novel bio-cement, a sustainable alternative that bypasses traditional high-temperature processing. Our approach leverages microbially induced calcite precipitation (MICP) in combination with a specific type of synthetic spider silk protein. We want to create a consortium of two bacteria types, a stone mason which crosslinks particles via MICP and a weaver that provides a micro-framework through the secretion of synthetic pyriform silk.
MICP, in which bacterial activity induces calcium carbonate (calcite) deposition, offers a promising approach for the development of cement alternatives (Castro-Alonso et al., 2019). This property is widespread across soil dwelling bacteria and even led to the development of mineral formations like stromatolites, which are fossilized bacteria (Allwood et al., 2006; Lowenstam, 1981). As there are a lot of bacteria with native high MICP activity, we use an environmental isolate shown to be highly efficient at precipitating calcite.
In recent history many MICP-based applications from soil consolidation, protection of beach erosions, dust prevention and the prominent self-healing concrete arose (Anbu et al., 2016; Reeksting et al., 2020). Even though many possible applications are being researched only little of them have been transformed to a commercial product successfully. This is due to the fact that the crosslinking of particles via MICP alone can be inconsistent: in porous or loosely packed materials, calcite does not always bridge gaps effectively as for example sand particles are too far away from each other, leading to weak bonding and consequently to weaker mechanical properties (Lai et al., 2024). Here our synthetic spider silk comes into play.
https://ipact.org.uk/projects/micp-for-repair-and-protection-of-coastal-assets/
Spiders do not make a single “silk” but a toolkit of silk types, each evolved for a particular task. Depending on the species, spiders can produce up to seven or more distinct silks, major-ampullate (dragline) for load-bearing threads, minor-ampullate for auxiliary lines, flagelliform for stretchy capture spirals, aciniform for prey-wrapping, tubuliform for egg sacs, aggregate glue for stickiness, and pyriform silk, which spiders use as an adhesive “cement” to join threads and anchor the web to substrates (Ramezaniaghdam et al., 2022).
These functional differences are encoded in the spidroin amino-acid motifs and block architectures: tensile silks are enriched in β-sheet-forming repetitive motifs, while adhesive silks (and their associated low-molecular co-proteins) contain different repeat chemistry, charge distribution and polar regions that underlie stickiness and interfacial bonding (Tokareva et al., 2013).
Spider silk is known for its extraordinary mechanical properties - stronger than steel, lightweight, biodegradable, and highly elastic (Gosline et al., 1999; Vollrath & Knight, 2001). Its applications span biomedicine, aerospace, smart materials, and biosensors (Ramezaniaghdam et al., 2022).
Our innovation lies in the use of pyriform silk, a lesser-studied type of silk. We selected pyriform silk deliberately because its biological role, forming attachment discs and cementing silk to surfaces, maps directly onto the functional need of a bio-cement scaffold.
Where dragline is optimized for strength and toughness, pyriform silk proteins (PySp1/PySp2) combine adhesive chemistry with some filamentous behaviour (Greco et al., 2020; Ramezaniaghdam et al., 2022), making them naturally suited to act as a micro-framework that binds particles and promotes mineral bridging. Recent sequencing and biochemical work on pyriform spidroins has revealed block modules and charged/polar regions that plausibly mediate adhesion and surface interactions (Wang et al., 2019), properties that are functionally advantageous for templating mineral deposition in MICP-based materials.
Pyriform silk offers an excellent functional match for a bio-cement scaffold because of its natural usage as microframework but still requires solving a set of classical recombinant protein problems compounded by large repetitive sequence architecture prior to the implementation.
Translating spider silk from spider glands into an industrial production pipeline is hard. There are two tightly linked classes of hurdles: genetic/assembly problems caused by the extreme repetitiveness of spidroin genes, and cellular/biophysical problems caused by expressing very large, repetitive, and sometimes aggregation-prone proteins in foreign hosts (Whittall et al., 2021).
At the DNA level, native spidroin genes contain long arrays of near-identical repeats. Traditional cloning strategies that rely on PCR or long single-fragment synthesis are prone to template slippage, mis-priming, deletions and recombination, which makes obtaining stable, full-length constructs difficult and time-consuming. Several reviews and experimental reports document how PCR-based multimerisation or head-to-tail strategies frequently yield truncated or rearranged constructs when repeat counts increase (Ramezaniaghdam et al., 2022; Tokareva et al., 2013).
Even with a correct DNA construct, translation and folding present further obstacles. Repetitive proteins impose unusual demands on the host translation machinery: skewed codon composition in native spidroins can cause local depletion of cognate tRNAs and ribosome stalling, which in turn can trigger quality-control pathways (e.g., proteolysis) and thereby reduce yields (Whittall et al., 2021). Codon usage therefore matters beyond “expression level”, it affects co-translational folding kinetics, the solubility and function of the polypeptide (Liu et al., 2021). Experimental and computational studies show that codon optimization must be handled carefully to avoid removing beneficial translational pauses required for correct folding, while supplementing rare tRNAs or engineering host tRNA pools can relieve bottlenecks in some systems (Angov et al., 2008).
Our Approach
To address these challenges, we developed a strategy we call “Pyricloning”, a PCR-free DNA assembly method that allows the rapid modular buildup of repetitive sequences from small, stable building blocks. Moreover, we fine tuned our sequences via codon harmonizing, an advancement of codon optimisation, to reduce translational issues (Angov et al., 2011). We aim to express our constructs in the well-known industrial workhorse B. subtilis to achieve a possible scalable production. We selected Bacillus subtilis as the primary expression host because it combines several practical advantages for an extracellular scaffold strategy: well-characterized secretion pathways, an extensive toolkit for genetic manipulation, a long industrial track record (including GRAS-status strains in some contexts), and simpler extracellular processing compared to many yeast systems (Schallmey et al., 2004; Souza et al., 2021). These properties make B. subtilis particularly suitable for testing secreted and surface-display silk architectures, and for designing scalable downstream processes.
By reducing interstitial spaces between sand particles, allowing bacteria to migrate better and deposit calcite more thoroughly, we believe that synthetic pyriform silk can significantly enhance MICP-based applications, ultimately leading to a reduced need of conventional construction materials with a high CO2 footprint.
Possible applications and implementations of our approach could be:
• Eco-friendly bricks and blocks: Replacing fired bricks with bio-cement eliminates the need for kilns.
• Self-healing concrete: Embedded bacteria and silk scaffolds could autonomously repair cracks, extending structural lifetime.
• Soil stabilization: Ideal for erosion control or foundation preparation in sandy soils.
Moving forward, our goals are twofold:
1. Scaling spider silk and bio-cement production, to test mechanical properties, durability, and real-world performance.
2. Expanding Pyricloning, promoting it as a standard for the synthetic biology community to enable stable assembly of other repetitive genes.
In the long run, Pyricon envisions a future where construction is no longer synonymous with carbon pollution, but instead driven by sustainable, bio-inspired materials.
Building on Prior Work
The iGEM team BOKU-Vienna 2022 attempted a similar direction, expressing MaSp1 dragline silk in Pichia pastoris as part of their “Pichitecture” project. Their work was innovative and ambitious, but it also illustrated key challenges:
• Their cloning relied on PCR, which is problematic for repetitive sequences.
• Dragline silk, while strong, is not optimized for adhesion or cementation.
• Their proof-of-concept results were preliminary, and construct flexibility was limited.
• P. pastoris posed expression and secretion hurdles for such large repetitive proteins.
We value their contribution as an important stepping stone but take a different path: choosing pyriform silk for its adhesive role, using B. subtilis as a secretion-friendly host, and employing Pyricloning to avoid PCR pitfalls. Together, these choices give our project both scientific novelty and practical advantages.
Our project shows how synthetic biology can tackle grand challenges. It not only addresses one of the world’s largest industrial CO₂ sources but also contributes a flexible genetic tool with applications beyond construction. By demonstrating a material that is strong, sustainable, and scalable, we hope to inspire new directions in both biotechnology and green architecture.
Integrated Human Practices
From the beginning of our project, we recognized that developing a bio-based cement alternative cannot be done in isolation. Cement and concrete are not just materials – they are the backbone of global infrastructure, with enormous economic, environmental, and societal implications. To ensure our work is both scientifically robust and socially relevant, we actively engaged with stakeholders from different fields and integrated their perspectives into our project design.
Engaging with Stakeholders
We consulted with civil engineers, material scientists, and members of the construction industry to understand real-world requirements for alternative building materials. Feedback emphasized that strength, scalability, and cost-competitiveness are non-negotiable for adoption. This helped us shape our project goals: rather than aiming only at proof-of-concept mineralization, we focused on improving the mechanical stability of bio-cement through the addition of spider silk as a structural scaffold.
Safety and Regulatory Considerations
Working with genetically modified organisms (GMOs) in open environments such as construction sites raises important safety questions. We discussed containment strategies and explored potential regulatory pathways for bio-based building materials. These conversations reinforced the need for clear kill-switch strategies and material processing steps that depending on the target market ensure no living GMOs are present in the final bricks or structures. By designing for safety from the start, we aim to make our approach compatible with environmental regulations and public acceptance.
Societal Impact and Sustainability
Our stakeholder interactions also highlighted the dual opportunity of our work: on the one hand, reducing CO₂ emissions from cement production; on the other hand, introducing a paradigm shift towards bio-inspired materials in construction. We positioned our project not as a direct competitor to cement in all contexts, but as a complementary material that could first find use in niche applications like eco-friendly bricks and erosion control. This incremental approach makes adoption more feasible and reduces the risks associated with radical industry transformation.
By integrating these perspectives, we designed Pyricon to be more than a technical solution. It is a project grounded in real-world needs, developed with awareness of environmental responsibility, and aligned with the broader vision of sustainable construction.
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