Gas Fermentation & Carbon Utilisation: Conversion of greenhouse gases and waste carbon. Carbon recycling.

Chief Investigator(s)

Esteban Marcellin, James Heffernan, Lars Puiman, Wei Jiang

Background and Need

Methane is a potent greenhouse gas generated from diverse industrial and biological activities, yet its direct utilisation remains technically challenging due to its chemical stability and the high costs associated with conventional conversion processes. Existing methane bioconversion pathways primarily generate low-value products such as biomass or polyhydroxybutyrate, limiting economic viability. There is therefore a strong need to develop biological platforms capable of converting methane into higher-value chemicals that support industrial decarbonisation and sustainable manufacturing.

Project Aim

The project aims to develop a stable microbial coculture platform capable of converting methane into isoprene through coordinated metabolic engineering of complementary microbial partners.

Approach and Key Activities

The project employs modular metabolic engineering of yeast strains to introduce and optimise isoprene biosynthesis pathways capable of sustained production. Parallel development of methanotrophic bacteria enables efficient methane oxidation and provision of metabolic intermediates required for coculture productivity. Coculture engineering strategies are implemented to stabilise microbial interactions and minimise inhibitory feedback effects. Bioreactor-level modelling and controlled cultivation experiments are conducted to define operating conditions that maximise productivity, maintain physiological compatibility, and support stable methane-to-isoprene conversion under scalable fermentation environments.

Expected Outcomes

The project will deliver engineered microbial strains capable of coordinated methane utilisation and isoprene biosynthesis within a stable coculture system. Additional outputs include validated cultivation protocols, early-stage coculture productivity datasets, and bioreactor operating strategies that support stable methane conversion performance suitable for scale-up and process optimisation.

Impact and Significance

This project establishes a foundation for producing sustainable isoprene from methane, enabling development of low-carbon alternatives for polymer and chemical industries. The outcomes support methane valorisation strategies aligned with industrial decarbonisation goals and create new opportunities for converting waste methane into higher-value chemicals suitable for existing industrial supply chains.

Keywords

• Adaptive laboratory evolution
• Bioprocess optimisation
• Gas fermentation
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Esteban Marcellin, James Heffernan, Lars Puiman

Background and Need

Global demand for plastics continues to increase, driving significant greenhouse gas emissions and environmental accumulation of non-biodegradable materials. While biological production of biodegradable polyhydroxybutyrate (PHB) from CO₂ offers a sustainable alternative, current gas fermentation processes rely on high hydrogen concentrations that introduce safety risks, increase operational costs, and limit scalability. There is therefore a need to develop microbial strains capable of efficient PHB production under safer, low-hydrogen operating conditions suitable for industrial deployment.

Project Aim

The project aims to engineer and evolve Cupriavidus necator H16 strains capable of efficient PHB production from CO₂ under low-hydrogen conditions suitable for scalable and safe gas fermentation processes.

Approach and Key Activities

Adaptive laboratory evolution strategies were applied under reduced hydrogen concentrations to identify genetic targets associated with improved metabolic efficiency. Targeted gene knockouts were performed to remove energy-consuming metabolic pathways and enhance carbon flux toward PHB accumulation. Systems-level investigations, including proteomic and metabolic network analysis, were conducted to improve understanding of cellular responses under varying gas fermentation conditions. Continuous gas fermentation experiments under oxygen-limited environments were implemented to validate strain performance and demonstrate feasibility of sustained PHB production.

Expected Outcomes

The project will deliver engineered microbial strains capable of enhanced PHB accumulation under low-hydrogen conditions and validated continuous gas fermentation strategies. Additional outputs include improved genome-scale metabolic models, identified metabolic engineering targets, and experimental datasets supporting scalable PHB production from CO₂ feedstocks.

Impact and Significance

This project supports development of low-carbon biodegradable plastic production technologies by enabling safe and scalable biological conversion of CO₂ into PHB. The outcomes benefit industrial sectors seeking sustainable materials and contribute to emissions reduction strategies by transforming waste carbon into valuable biodegradable products aligned with circular bioeconomy objectives.

Keywords

• Adaptive laboratory evolution
• Bioprocess optimisation
• Bioreactor engineering
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Esteban Marcellin, James Heffernan, Lars Puiman

Background and Need

Industrial waste gases containing CO₂, CO, H₂, and CH₄ represent an underutilised carbon resource that contributes significantly to greenhouse gas emissions. Current microbial platforms are limited in their ability to simultaneously utilise multiple one-carbon substrates, reducing process flexibility and overall efficiency. Developing microbial systems capable of metabolising diverse C1 substrates is therefore essential to enable full utilisation of mixed waste gases and improve the economic viability of gas fermentation technologies across industrial sectors.

Project Aim

The project aims to develop Hydrogenophaga pseudoflava as a versatile microbial chassis capable of converting multiple one-carbon substrates, including CO₂, CO, H₂, formate, and methanol, into valuable bioproducts.

Approach and Key Activities

The project investigates the native autotrophic metabolism of Hydrogenophaga pseudoflava to characterise its growth performance across different gaseous substrate combinations. Genetic engineering strategies were implemented to introduce non-native enzymes enabling utilisation of additional substrates such as formate and methanol. Adaptive laboratory evolution was applied to improve growth rates and metabolic efficiency on engineered pathways. Experimental validation included growth optimisation under controlled gas mixtures and evaluation of biopolymer production performance, providing insight into metabolic flexibility and pathway efficiency under scalable fermentation conditions.

Expected Outcomes

The project will deliver engineered microbial strains capable of utilising expanded one-carbon substrate ranges, along with validated growth and production datasets across mixed gas environments. Additional outputs include improved metabolic pathway configurations, adaptive evolution-derived strains with enhanced performance, and experimentally validated strategies for efficient multi-substrate gas fermentation.

Impact and Significance

This project enables more complete utilisation of mixed industrial waste gases by developing flexible microbial platforms capable of converting diverse carbon sources into valuable products. The outcomes support industrial decarbonisation strategies, improve resource efficiency, and strengthen the technological foundation required for scalable and economically viable gas fermentation processes across multiple industrial applications.

Keywords

• Adaptive laboratory evolution
• Biomaterials & biopolymers
• Bioprocess optimisation
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Esteban Marcellin, James Heffernan, Lars Puiman

Background and Need

Growing global demand for protein is placing significant pressure on land, water, and agricultural systems, while large volumes of biogas and waste methane remain underutilised. Conventional protein production systems rely heavily on resource-intensive agriculture and contribute substantially to greenhouse gas emissions. There is therefore a need to develop alternative protein production systems capable of converting waste gases into sustainable microbial biomass suitable for food and feed applications while reducing environmental impact.

Project Aim

The project aims to develop a scalable gas fermentation platform capable of converting methane-rich biogas into microbial biomass suitable for sustainable protein production.

Approach and Key Activities

The project focuses on the development of microbial cultivation strategies capable of converting methane into biomass under controlled gas fermentation conditions. Methanotrophic microbial systems are evaluated for growth performance and nutrient conversion efficiency across different gas compositions representative of industrial biogas streams. Bioprocess optimisation is conducted to improve productivity and biomass yield through controlled gas supply, nutrient balance, and reactor operation. Downstream characterisation of biomass composition is performed to assess protein content and suitability for food and feed applications.

Expected Outcomes

The project will deliver validated microbial cultivation processes capable of producing protein-rich biomass from methane-based feedstocks. Additional outputs include optimised gas fermentation conditions, performance datasets describing biomass productivity and composition, and validated strategies supporting integration of methane-based protein production into scalable industrial processes.

Impact and Significance

This project supports development of sustainable protein production technologies by enabling conversion of waste methane into valuable nutritional products. The outcomes benefit food and feed industries seeking low-emission protein sources while reducing reliance on conventional agriculture and contributing to improved resource efficiency and greenhouse gas mitigation strategies.

Keywords

• Adaptive laboratory evolution
• Bioprocess optimisation
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Precision fermentation
• Process scale-up & pilot plant
• Waste valorisation

Chief Investigator(s)

Esteban Marcellin, James Heffernan, Lars Puiman

Background and Need

Sustainable aquaculture requires reliable alternatives to fishmeal and fish oil, which currently depend heavily on wild fisheries and face increasing environmental and supply instability. At the same time, biogas containing methane and CO₂ represents an abundant renewable resource that remains underutilised due to the lack of biological systems capable of efficiently converting both gases into valuable biomass. There is therefore a need to develop integrated microbial platforms that convert waste gases into nutrient-rich feed ingredients supporting circular and low-carbon food production systems.

Project Aim

The project aims to develop an integrated gas fermentation platform capable of converting methane and CO₂ from biogas into sustainable, protein-rich microbial biomass suitable for aquaculture feed applications.

Approach and Key Activities

The project develops a synthetic microbial consortium designed to enable simultaneous utilisation of methane and CO₂ through coordinated metabolic processes supported by renewable hydrogen inputs. Microbial strain selection and engineering are performed to optimise nutrient production and biomass composition, including enrichment of omega-3 fatty acids and carotenoid compounds. Bioprocess optimisation is conducted through controlled gas fermentation experiments to stabilise microbial interactions and maximise productivity. Integrated reactor operation strategies are evaluated to establish a scalable “one-pot” fermentation system suitable for continuous feed production.

Expected Outcomes

The project will deliver a validated microbial consortium capable of converting biogas into protein-rich biomass suitable for aquaculture feed applications. Additional outputs include defined reactor operating conditions, optimised microbial cultivation protocols, and performance datasets demonstrating production of nutritionally enriched biomass containing omega-3 fatty acids and functional metabolites relevant to commercial feed applications.

Impact and Significance

This project supports the transition toward sustainable aquaculture by providing a renewable alternative to fishmeal derived from wild fisheries. The outcomes benefit aquaculture and feed industries by reducing reliance on conventional marine resources while enabling circular use of waste gases. The project contributes to greenhouse gas mitigation and strengthens industrial capability to produce sustainable feed ingredients using scalable gas fermentation technologies.

Keywords

• Adaptive laboratory evolution
• Bioprocess optimisation
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Precision fermentation

Chief Investigator(s)

Esteban Marcellin, James Heffernan, Lars Puiman

Background and Need

Methane represents a significant greenhouse gas and an underutilised carbon resource, yet efficient biological conversion platforms remain limited by the availability of robust methanotroph strains and well-characterised methane monooxygenase (MMO) enzymes. Existing methane bioconversion systems lack scalable screening tools and reliable strain discovery pipelines, restricting development of methane-to-value technologies. There is therefore a need to establish integrated platforms combining enzyme engineering, strain discovery, and screening technologies to enable efficient methane utilisation and support development of methane-derived bioproducts.

Project Aim

The project aims to develop an integrated platform for methane bioconversion through engineering methane monooxygenase enzymes, discovering novel methanotrophs, and establishing scalable screening and cultivation strategies.

Approach and Key Activities

The project established a high-throughput screening platform including construction of a methanol biosensor plasmid to enable functional characterisation of methane oxidation activity. Computational reconstruction of ancestral methane monooxygenase enzymes was performed to support enzyme engineering workflows, followed by cloning and functional testing. Methanotrophic and methylotrophic microbial communities were enriched from environmental samples collected from wetlands, enabling identification of novel methane-oxidising organisms. Proof-of-concept cultivation studies were conducted, including microbial growth under simulated microgravity conditions, supporting development of scalable methane bioconversion systems.

Expected Outcomes

The project will deliver functional methane monooxygenase engineering pipelines, validated methanol biosensor screening tools, and enriched methanotrophic microbial communities capable of methane utilisation. Additional outputs include experimental datasets supporting methane consumption performance and demonstration of proof-of-concept methane-to-protein and methane-to-biopolymer production pathways.

Impact and Significance

This project supports development of scalable methane-to-X biomanufacturing technologies by enabling discovery and optimisation of high-performing methanotrophs and enzyme systems. The outcomes strengthen capability to convert methane into valuable products such as proteins and biopolymers, contributing to greenhouse gas mitigation and supporting industrial deployment of biological methane utilisation platforms.

Keywords

• Bioprocess optimisation
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Birgitta Ebert, Esteban Marcellin, Muxina Konarova, Lalevash Moghaddam, Darryn Rackemann, Leonie van’t Hag

Background and Need

Reducing emissions from fuels and materials requires new ways to use carbon that do not rely on fossil resources or compete with food production. While biological systems can convert carbon dioxide efficiently, they rarely produce fuels or hydrocarbons directly. To make carbon utilisation practical at scale, biological carbon capture needs to be combined with downstream upgrading steps that turn simple intermediates into usable fuels and industrial products.

Project Aim

The project aims to develop an integrated two‑stage process that converts carbon dioxide into fuel‑range hydrocarbons and intermediates suitable for aviation fuel, lubricants, and related applications.

Approach and Key Activities

The project adopts a modular, integrated approach combining biological carbon fixation, microbial upgrading, and downstream chemical refinement. Carbon dioxide is first converted into low‑molecular‑weight intermediates through anaerobic gas fermentation, which are subsequently upgraded via aerobic conversion with engineered Pseudomonas strains into higher‑value oxygenated compounds. These intermediates are then chemically refined into hydrocarbons and functional materials. This project combines microbial cell engineering, bioprocess development, and chemical upgrading to establish a scalable carbon‑to‑fuels pathway.

Expected Outcomes

The project will deliver a two‑stage process for chemo‑biocatalytic conversion of carbon dioxide into hydrocarbon intermediates and refined fuel products. Outcomes include optimised biological conversion routes, effective integration of fermentation and chemical upgrading, and performance data relevant to fuel and materials applications. The results will support scale‑up considerations, techno‑economic analysis, and future deployment within carbon‑utilisation value chains.

Impact and Significance

The project advances carbon utilisation by demonstrating practical routes for converting carbon dioxide into aviation fuels and industrial products, directly supporting SDG 9 (Industry, Innovation and Infrastructure). By treating waste carbon as a resource, it contributes to SDG 12 (Responsible Consumption and Production) and enables evidence‑based evaluation of decarbonisation pathways relevant to SDG 13 (Climate Action). Strong industry involvement further supports collaborative innovation under SDG 17 (Partnerships for the Goals).

Keywords

• Adaptive laboratory evolution
• Biomaterials & biopolymers
• Bioprocess optimisation
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Denys Villa Gomez, Esteban Marcellin, Axayacatl Gonzalez

Background and Need

Methane is a potent greenhouse gas, yet current mitigation approaches often lack efficiency, scalability, or biological stability under real‑world conditions. Existing methane oxidation systems are typically derived from non‑local or poorly adapted microbial communities, limiting performance in diverse environments. Improving biologically driven methane removal is critical for reducing industrial emissions, supporting sustainable fertiliser production, and advancing climate change mitigation strategies across sectors such as mining, waste management, and agriculture.

Project Aim

This project aims to optimise and scale methane‑oxidising Australian microbial consortia for efficient, industrially relevant methane mitigation and biomass production under controlled fermentation conditions.

Approach and Key Activities

The project integrates microbial ecology, bioprocess engineering, and analytical chemistry to scale methane‑oxidising consortia. Australian methanotrophic communities will be optimised in lab‑scale batch and continuous bioreactors simulating dilute methane streams. Scale‑up processes will be refined through controlled fermentation, including operation of a 15 L bioreactor. Metabolic activity will be monitored using HPLC and GC‑MS for gas and metabolite analysis, alongside carbon–nitrogen and nutrient balancing. Metagenomic sequencing will track microbial composition, enabling iterative optimisation of growth conditions, productivity, and system stability.

Expected Outcomes

The project will deliver an optimised fermentation scale‑up process for methane‑oxidising consortia, validated in a 15 L bioreactor system. Outputs include production of liquid cultures equivalent to 200 g of dried biomass, detailed metabolic and gas analysis datasets, and microbial community profiles over time. These results will establish reproducible protocols for biomass production and performance benchmarks for industrial deployment.

Impact and Significance

This work will benefit industries seeking cost‑effective methane mitigation, including mining, agriculture, and waste management. By enabling scalable, locally adapted microbial solutions, the project supports emissions reduction and sustainable fertiliser production. It strengthens Australia’s capability in environmental biotechnology and provides industry‑ready processes that can be integrated into existing methane capture and utilisation systems, contributing to national and global climate goals.

Keywords

• Bioprocess optimisation
• Bioreactor engineering
• Environmental engineering

Chief Investigator(s)

Esteban Marcellin, Wei Jiang

Background and Need

Methane and carbon dioxide are major greenhouse gases generated from industrial and agricultural processes, yet current technologies for their utilisation remain inefficient and energy‑intensive. Biogas, composed of methane and CO₂, is often underutilised due to the need for costly gas separation and limited biological systems capable of co‑utilising both gases. There is therefore a need to develop integrated microbial systems capable of converting biogas directly into high‑value products such as sustainable animal feed.

Project Aim

The project aims to develop an integrated microbial synthetic consortium capable of co‑consuming methane and CO₂ from biogas and converting these gases into sustainable fish meal replacement products.

Approach and Key Activities

The project develops a synthetic microbial community consisting of hydrogenotrophs and methanotrophs capable of co‑utilising methane and CO₂ without requiring costly gas purification. Engineered yeasts are designed to consume fermentation byproducts and produce omega‑3 fatty acids and astaxanthin to enhance nutritional value. Bioprocess optimisation strategies are applied to control hydrogen, oxygen, and temperature to stabilise microbial interactions and maximise productivity. Techno‑economic analysis and process modelling are conducted to evaluate scalability and economic feasibility of the integrated one‑pot fermentation system.

Expected Outcomes

The project will deliver a validated synthetic microbial consortium capable of converting biogas into protein‑rich biomass enriched with omega‑3 fatty acids and astaxanthin. Additional outputs include defined operating conditions for stable co‑culture performance, techno‑economic assessments of process feasibility, and scalable bioprocess strategies supporting industrial implementation of sustainable fish meal production.

Impact and Significance

This project supports the transition toward low‑carbon industrial systems by enabling direct conversion of methane and CO₂ into sustainable aquaculture feed products. The outcomes contribute to reducing greenhouse gas emissions, improving resource efficiency, and establishing scalable biological solutions aligned with national decarbonisation strategies and the development of a circular bioeconomy.

Keywords

• Adaptive laboratory evolution
• Bioprocess optimisation
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Precision fermentation
• Process scale-up & pilot plant
• Synthetic biology & strain engineering

Chief Investigator(s)

Esteban Marcellin, Birgitta Ebert

Background and Need

Biological conversion of CO₂ and H₂ into acetate using acetogenic bacteria offers a promising route for sustainable fuel and chemical production. However, current acetogenic platforms remain limited by suboptimal growth rates, strain robustness, and insufficient integration with downstream production pathways. Efficient selection of high‑performing acetogens and development of scalable fermentation strategies are therefore required to enable reliable CO₂‑to‑chemicals conversion and support industrial implementation of gas fermentation technologies.

Project Aim

The project aims to identify high‑performing acetogenic strains and develop evolved platforms and bioprocess strategies enabling efficient CO₂ and H₂ conversion into acetate for downstream chemical production.

Approach and Key Activities

The project evaluates growth performance of acetogenic strains including Acetobacterium woodii, Thermoanaerobacter kivui, and Moorella thermoacetica under defined anaerobic conditions. Selected strains are characterised in serum bottles and bioreactors to assess gas uptake, growth behaviour, and acetate production. Adaptive laboratory evolution and random mutagenesis strategies are implemented to improve strain performance, including temperature adaptation and robustness enhancement. Two‑stage fermentation processes are developed to convert acetate produced by acetogens into higher‑value products such as methyl ketones, supported by analytical measurements including off‑gas analysis, metabolomics, proteomics, and genome sequencing.

Expected Outcomes

The project will deliver characterised and evolved acetogenic strains demonstrating improved growth and acetate production performance. Additional outputs include validated two‑stage fermentation workflows, defined operating conditions for CO₂ and H₂ fermentation, and datasets describing gas uptake, metabolic behaviour, and product formation under controlled bioreactor conditions.

Impact and Significance

This project supports development of scalable CO₂‑to‑chemicals platforms by improving acetogen performance and enabling integration of upstream gas fermentation with downstream product synthesis. The outcomes contribute to advancing sustainable chemical production technologies and strengthen the technical foundation required for industrial deployment of biological carbon conversion processes.

Keywords

• Bioprocess optimisation
• Bioreactor engineering
• Gas fermentation
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Yosephine Gumulya, Esteban Marcellin

Background and Need

Anthropogenic methane emissions are rising at an alarming rate, surpassing the capacity of natural sinks to mitigate them. Synthetic methanotrophs offer a scalable, controllable, and technology‑driven solution that can directly capture and convert methane into value‑added products such as single‑cell protein or biochemicals — turning harmful emissions into an economic opportunity.

Project Aim

This project aims to engineer synthetic methanotrophs by integrating computational enzyme design, high‑throughput screening, and directed evolution to develop novel methane monooxygenase enzymes with enhanced catalytic performance. A transcription factor–based biosensor will be created to enable high‑throughput screening of enzyme libraries. The optimised enzymes will be integrated into yeast, establishing a robust microbial platform capable of upcycling methane into sustainable alternative proteins.

Expected Outcomes

The project will deliver engineered methane monooxygenase variants with significantly improved catalytic efficiency, a validated methanol‑responsive biosensor for high‑throughput screening, optimised synthetic methanotroph yeast strains, and demonstration of methane‑to‑protein conversion at bioreactor scale. This work transforms methane from a harmful greenhouse gas into a valuable protein resource, supporting climate mitigation and food security. It benefits energy industries seeking decarbonisation solutions, strengthens Australia’s circular bioeconomy capability, and reduces reliance on imported protein feeds. The platform also establishes a foundation for broader methane‑to‑chemicals biomanufacturing.

Keywords

• Gas fermentation
• Synthetic biology & strain engineering

Chief Investigator(s)

Yosephine Gumulya, Carlos Acevedo Rocha, Silvia Osuna, Esteban Marcellin

Background and Need

Methane is a potent greenhouse gas, yet converting it into useful products remains inefficient. Industrial routes typically require high temperatures and complex infrastructure, while enzyme‑based oxidation is still far from practical because designed catalysts often show very low activity and methane readily escapes from active sites. Current enzyme design algorithms miss essential elements — electrostatics, precise active‑site pre‑organisation, and protein dynamics — limiting progress toward scalable methane‑to‑methanol biocatalysis.

Project Aim

The project aims to design, build, and validate Compound I–based methane monooxygenases by combining computation‑guided active‑site and tunnel redesign with wet‑lab screening, extending improvements from P450 scaffolds to self‑sufficient UPO enzymes.

Approach and Key Activities

WP1 uses molecular dynamics and co‑evolutionary/Potts‑guided combinatorial design to compress and hydrophobise the P450PMO active site and narrow access tunnels, retaining methane near Compound I for C–H activation. WP2 mines compact UPO scaffolds with suitable hydrophobic active sites using structure‑based searches (e.g., Foldseek), then transfers and adapts key P450PMO/P450MMO design features to create UPOPMO/UPOMMO variants. WP3 expresses P450 variants in E. coli and UPOs in Pichia pastoris, quantifies methane oxidation by headspace GC‑FID, and applies ML‑guided directed evolution (ProteusAI) if needed to increase activity.

Expected Outcomes

The project will deliver computationally prioritised P450MMO and UPO candidate enzymes with experimentally validated methane oxidation activity measured by quantitative headspace GC. It will establish a repeatable design‑to‑test workflow linking MD/co‑evolutionary designs to wet‑lab performance, alongside improved propane‑oxidation controls and a portfolio of engineered UPO scaffolds suitable for further optimisation.

Impact and Significance

By turning methane oxidation into an engineerable, testable enzyme‑design problem, this project can accelerate low‑temperature methane valorisation and open routes to distributed, lower‑carbon methanol production. Outcomes benefit enzyme engineering and biomanufacturing communities seeking selective C–H oxyfunctionalisation catalysts, while contributing to environmental goals by enabling technologies that convert methane emissions into valuable chemical feedstocks.

Keywords

• Computational biology & AI
• Synthetic biology & strain engineering

Chief Investigator(s)

Tim McCubbin, Esteban Marcellin, Paul Webley

Background and Need

Photobioreactor scale‑up is limited by declining light penetration at high cell densities, accumulation of dark‑respiration losses, and inefficient gas exchange. These constraints reduce photosynthetic productivity and hinder industrial deployment. Although cyanobacteria offer rapid growth and adaptability for sustainable biomanufacturing, existing reactor designs and operating strategies struggle to maintain performance at scale, limiting their industrial and environmental impact.

Project Aim

The aim of this project is to optimise photobioreactor design and cyanobacterial metabolism to enable continuous, high‑productivity sugar synthesis using light and alternative substrates as redox sources, coupled with more energetically efficient carbon‑fixation pathways.

Approach and Key Activities

This project integrates reactor engineering and systems biology to address photobioreactor scale‑up challenges. Computational fluid dynamics (CFD) will be used to design and optimise photobioreactors, improving light distribution and gas exchange under continuous operation. Cyanobacteria will be cultivated under aerobic, anaerobic, light‑driven, and alternative redox‑source‑driven conditions. Comprehensive multi‑omics analyses will identify metabolic and regulatory bottlenecks affecting growth and productivity. Guided by these data, metabolic engineering strategies will redirect carbon flux toward sugar production, supported by CFD‑informed reactor operation and metabolic modelling.

Expected Outcomes

The project will deliver optimised photobioreactor designs, validated CFD models, and stable continuous cultivation protocols. Additional outcomes include systems‑level metabolic maps, engineered cyanobacterial strains with enhanced sugar productivity, more efficient carbon‑fixation pathways, and integrated datasets linking reactor conditions, metabolism, and product formation across light‑ and alternative‑redox‑cofactor‑driven growth modes.

Impact and Significance

This research will enable scalable, continuous production of bio‑based sugars using cyanobacteria, supporting low‑carbon manufacturing and resource‑efficient bioprocesses. Outcomes will benefit industrial biotechnology by improving reactor performance and metabolic efficiency, while advancing fundamental understanding of photosynthetic metabolism. The work contributes to sustainable chemical production and strengthens photobioreactor design capabilities.

Keywords

• Adaptive laboratory evolution
• Bioprocess optimisation
• Bioreactor engineering
• Computational biology & AI
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Tim McCubbin

Background and Need

Cyanobacteria offer a sustainable platform for chemical production by using CO₂ and light as carbon and energy sources. However, industrial application is limited by self‑shading, where light penetration rapidly declines even at modest cell densities. This constraint reduces photosynthetic efficiency and productivity, making current metabolic and reactor strategies insufficient for scalable, light‑limited bioprocesses with meaningful environmental impact.

Project Aim

The aim of this project is to enhance cyanobacterial growth and productivity under light limitation by engineering energetically and kinetically efficient synthetic one‑carbon fixation pathways.

Approach and Key Activities

This project applies metabolic modelling and synthetic biology to redesign cyanobacterial carbon fixation. Alternative C1‑fixation pathways will be computationally designed and screened using whole‑database analyses based on ATP demand, thermodynamics, enzyme kinetics, oxygen sensitivity, and pathway complexity. Promising pathways will be integrated into genome‑scale metabolic models to prioritise candidates for strain construction. Engineered strains will be physiologically characterised using photophysiology, flow cytometry, proteomics, and metabolomics, followed by adaptive laboratory evolution to optimise pathway utilisation under light‑limited conditions.

Expected Outcomes

Expected outcomes include rationally designed synthetic C1‑fixation pathways, engineered cyanobacterial strains with improved growth under light limitation, validated metabolic models, and multi‑omics datasets identifying bottlenecks and optimisation targets. The project will also determine whether synthetic carbon fixation pathways can function independently of the Calvin–Benson–Bassham cycle.

Impact and Significance

This work advances sustainable biomanufacturing by improving light‑limited growth and carbon efficiency in cyanobacteria. Outcomes will enable higher productivity at lower light intensities, reducing energy input and reactor footprint. The project benefits industrial biotechnology and carbon‑negative manufacturing while providing fundamental insights into alternative carbon fixation and photosynthetic metabolism.

Keywords

• Adaptive laboratory evolution
• Computational biology & AI
• Gas fermentation
• Metabolic modelling
• Multi-omics analysis
• Synthetic biology & strain engineering

Chief Investigator(s)

Isabella Casini, Axayacatl Gonzalez, Tim McCubbin

Background and Need

Current bioprocesses rely heavily on sugar‑based feedstocks, limiting sustainability and increasing competition with food resources. Gas fermentation using methanogens offers a promising alternative by converting low‑cost gases such as CO₂ and H₂ into valuable products. However, limited understanding of methanogen metabolism, energy conservation, and process optimisation constrains industrial application. Advancing systems‑level knowledge is essential to unlock their potential as efficient, scalable microbial cell factories.

Project Aim

To develop a systems‑level understanding of methanogen metabolism to enable optimised gas fermentation processes and establish robust microbial cell factories for sustainable production of value‑added compounds.

Approach and Key Activities

The project will integrate fermentation experiments with multi‑omics and systems biology to characterise and optimise methanogen‑based bioprocesses. New fermentation datasets will be generated under varying substrate feeding strategies to improve and constrain genome‑scale metabolic models. Advanced omics analyses, including proteomics and intracellular metabolomics, will provide insights into energy conservation and metabolic fluxes. These data will support development of predictive and kinetic models to identify bottlenecks, guide genetic engineering, and optimise carbon partitioning between biomass and product formation under continuous cultivation conditions.

Expected Outcomes

The project will deliver expanded multi‑omics datasets, including the first intracellular metabolomics for M. thermautotrophicus, improved genome‑scale and kinetic models, and optimised gas fermentation strategies. It will also identify metabolic bottlenecks and engineering targets, providing a framework for developing methanogens as versatile microbial cell factories for diverse industrial applications.

Impact and Significance

This project supports Australia’s transition to sustainable biomanufacturing by enabling the use of gaseous feedstocks for producing high‑value products. It benefits industry by reducing reliance on agricultural inputs and lowering environmental impact. Broader impacts include advancing sovereign capability in gas fermentation, fostering innovation through NCRIS infrastructure, and positioning Australia as a leader in carbon‑smart, next‑generation bioprocessing technologies.

Keywords

• Computational biology & AI
• Gas fermentation
• Metabolic modelling
• Process scale‑up & pilot plant
• Synthetic biology & strain engineering

Chief Investigator(s)

Denys Villa Gomez, Esteban Marcellin, Axayacatl Gonzalez Garcia, Yicheng Ma

Background and Need

Landfill methane emissions are a major contributor to greenhouse gas outputs, yet current mitigation approaches rely heavily on passive gas‑capture systems that are often inefficient or incomplete. Biological methane oxidation offers a scalable alternative capable of reducing fugitive emissions. Developing robust microbial consortia adapted to Australian landfill environments is therefore critical to enable reliable methane mitigation strategies that support industrial decarbonisation and environmental compliance.

Project Aim

To develop and deploy methane‑oxidising microbial consortia capable of reducing landfill methane emissions under representative field conditions relevant to industrial waste‑management environments.

Expected Outcomes

Validated methane‑oxidising microbial consortia suitable for landfill deployment. Demonstrated methane‑emission reduction under controlled landfill‑trial conditions. Quantified methane‑oxidation performance metrics. Established protocols for microbial enrichment and deployment. Generation of datasets supporting scale‑up and translation of methane‑mitigation strategies to operational landfill environments.

Impact and Significance

This project supports industrial methane mitigation by enabling biological treatment of landfill emissions. Waste‑management operators benefit through improved compliance and reduced greenhouse gas emissions. The approach contributes to national decarbonisation targets and establishes microbial methane mitigation as a viable strategy for large‑scale environmental emission‑reduction programs.

Keywords

• Bioprocess optimisation
• Bioreactor engineering
• Environmental engineering
• Gas fermentation
• Process scale‑up & pilot plant

Chief Investigator(s)

Gary Schenk, Anne Meyer

Background and Need

To mitigate global warming, reducing greenhouse gas emissions through the capture and conversion of carbon dioxide is essential. Current natural metabolic pathways are often inefficient for industrial applications. While a three‑enzyme cascade can convert CO₂ to methanol, the final step involving alcohol dehydrogenase (ADH) is a bottleneck. Existing yeast‑derived ADHs are structurally fragile, kinetically inefficient, and highly sensitive to methanol product inhibition.

Project Aim

This project aims to engineer robust, high‑efficiency alcohol dehydrogenase enzymes through genomic mining and ancestral reconstruction to optimise a cell‑free biocatalytic cascade for converting carbon dioxide into methanol.

Approach and Key Activities

The strategy combines bioinformatics and wet‑lab experimentation. Researchers will perform systematic genomic space exploration and Ancestral Sequence Reconstruction (ASR) to identify smaller, monomeric, and robust ADH variants. Key activities include high‑throughput recombinant production in E. coli and Pichia pastoris, followed by rigorous kinetic characterisation and robustness assessments against formaldehyde and methanol. Finally, the project integrates these optimised enzymes into a three‑step reaction cascade, using advanced electrochemical and spectral characterisation tools to validate performance and scalability.

Expected Outcomes

The project will deliver a portfolio of novel, engineered ADH enzymes with superior catalytic efficiency and product tolerance. Outputs include validated protocols for cell‑free CO₂‑to‑methanol conversion, high‑resolution structural predictions, and comprehensive kinetic datasets. Collaboration with DTU will generate joint publications and establish a framework for upscaling cell‑free enzyme reaction cascades for the bioeconomy.

Impact and Significance

The manufacturing sector benefits from a sustainable, cell‑free platform for producing green methanol, a critical chemical feedstock. This research supports global climate goals by providing innovative pathways for CO₂ utilisation. The strategic alliance between DTU and UQ establishes an international leadership hub in biotransformations, training specialised researchers to drive the emerging global bioeconomy.

Keywords

• Bioprocess optimisation
• Cell-free biomanufacturing
• Multi-omics analysis
• Waste valorisation