Environment & Agriculture: Engineered microbes. Biological solution for soils, crop resilience and productivity.
Around one-third of the world’s soils are degraded, threatening food production and reducing resilience to climate change.
This declining soil health limits nutrient availability, weakens crop performance and increases vulnerability to environmental stress.
The UQ Biosustainability Hub is finding and selecting beneficial microbes that enhance nutrient cycling and restore essential soil functions. These microbial communities improve the availability of key nutrients and support the recovery of soil biological activity.
These living soil technologies help rebuild soil fertility, support stronger and more resilient crops, and reduce dependence on synthetic fertilisers, contributing to more sustainable agricultural systems.
Biohub Environment & Agriculture Projects
Biodegradable and bioderived coatings for controlled release fertilisers
Chief Investigator(s)
Bronwyn Laycock, Susanne Schmidt, Steven Pratt, Paul A Lant, Ian Levett
Given the need to feed 9.7 billion people by 2050, it is vital to create a sustainable agricultural system. However, our current, essential fertilizer use has caused significant environmental challenges due to nutrient solubility. Better nutrient use efficiency is urgently required. Yet current coated fertilizers produce nondegradable microplastic residues. This project will deliver the first bioderived and biodegradable thin polymer coatings for high-efficiency fertilizers using innovative polyurethane chemistry, reactive extrusion processes, and in-house coating technologies. Nutrient release and transformations in soil and water will be quantified and modelled, along with plant yields, leading to advanced, sustainable fertiliser products.
Biofunctional spider silk for sustainable water treatment and resource recovery
Chief Investigator(s)
Birgitta Ebert, Gary Schenk, Thomas Schebel, Volker Sieber
Background and Need
Increasing contamination of wastewater and industrial emissions by pharmaceuticals, organo‑halides, and industrial chemicals threatens ecosystems, public health, and water security. Conventional treatment technologies often fail to remove persistent pollutants or recover valuable resources such as critical metals. The global transition from wastewater treatment to circular resource recovery requires innovative, multifunctional materials capable of simultaneous pollutant removal and resource capture under sustainable operating conditions.
Project Aim
The project aims to develop a biohybrid membrane filtration platform based on biofunctionalised recombinant spider silk for efficient pollutant degradation and selective resource recovery from wastewater and industrial off‑gas streams.
Approach and Key Activities
The project combines materials engineering, biocatalysis, and synthetic biology to fabricate spider‑silk‑based membranes functionalised with enzymes, peptides, and engineered living materials (ELMs). Recombinant spider silk membranes will be loaded with catalytic proteins for degradation of pharmaceuticals, antibiotics, phenolics, and organohalides, as well as metal‑binding proteins for selective rare‑earth‑element capture. Covalently immobilised microbial cells will enable sustained biotransformation. The approach leverages Bayreuth’s silk‑production platform and integrates UQ and TUM expertise in enzyme design, biochelation, and ELM engineering.
Expected Outcomes
The project will deliver proof‑of‑concept (TRL 4) silk‑based biohybrid membranes for pollutant degradation and metal recovery. Outputs include enzyme‑ and ELM‑functionalised filtration membranes, validated removal of pharmaceuticals, organohalides, and phenolics, and selective binding of rare earth elements, demonstrating scalability for wastewater and industrial‑emission treatment.
Impact and Significance
The project advances sustainable water management by enabling simultaneous detoxification and resource recovery, supporting circular‑bioeconomy principles. It benefits water, mining, chemicals, and environmental‑biotechnology sectors through deployable biofunctional materials. By reducing pollutant release, antimicrobial‑resistance risks, and critical‑metal losses, the project supports UN SDGs 6 and 12, delivering environmental, economic, and societal value.
Keywords
- Biomaterials & biopolymers
- Environmental engineering
- Synthetic biology & strain engineering
- Wastewater treatment
Seaweed microbiome as a source of high-value bioactives: vitamin B12, omega-3 fatty acids and skincare peptides
Chief Investigator(s)
Zeinab Khalil, Amila Agampodi Dewa
Background and Need
Seaweed‑associated microbiomes represent an unexplored reservoir of high‑value bioactive compounds including vitamins, fatty acids, and bioactive peptides. Global demand for sustainable, marine‑derived sources of vitamin B12, omega‑3 fatty acids, and natural skincare actives is rapidly increasing, driven by dietary shifts away from animal products and consumer preference for natural cosmetic ingredients. Current production methods are environmentally intensive and costly.
Project Aim
To characterise the seaweed microbiome and identify microbial strains and pathways responsible for producing vitamin B12, omega‑3 fatty acids, and bioactive peptides for skincare applications.
Approach and Key Activities
BLOOM will profile the microbiome of Australian seaweed species using metagenomics and metabolomics, identify biosynthetic gene clusters responsible for target‑compound production, isolate and culture productive microbial strains, and optimise production conditions. Bioactive peptides will be screened for skincare‑relevant activities, including anti‑inflammatory and collagen‑stimulating properties, in collaboration with Venus Shell Systems.
Expected Outcomes
A characterised seaweed‑microbiome catalogue; identified microbial producers of vitamin B12 and omega‑3 fatty acids; validated skincare‑peptide candidates; joint intellectual property; and a roadmap for sustainable marine‑bioactive production.
Impact and Significance
This project creates sustainable, marine‑derived alternatives to animal‑ and petrochemical‑based sources of high‑value ingredients, benefiting the nutraceutical, food, and cosmetics industries. It also supports development of a blue bioeconomy in Australia, leveraging unique marine biodiversity for commercial and environmental benefit.
Keywords
- Microbiome engineering & biodiscovery
- Multi-omics analysis
Discovery of novel agrochemicals from Australian soil and marine microbes
Chief Investigator(s)
Background and Need
Conventional synthetic agrochemicals face increasing regulatory restrictions due to environmental toxicity, resistance development, and harm to non‑target organisms. The agricultural sector urgently needs new, naturally derived crop‑protection agents with novel modes of action. Australian microbiomes — among the most diverse and underexplored globally — represent an exceptional source of novel bioactive molecules with agrochemical potential.
Project Aim
To discover and develop novel microbial natural products from Australian microbiomes with activity as sustainable agrochemicals for crop and animal protection.
Approach and Key Activities
BLOOM will apply its established biodiscovery platform, combining MATRIX microbioreactor cultivation, NOMETA activation of silent gene clusters, and multi‑omics profiling, to screen Australian soil and marine microbial isolates for agrochemically relevant bioactivity. Lead compounds will be isolated, structurally characterised, and evaluated for efficacy and selectivity in partnership with NovoNordisk, with a focus on compounds exhibiting novel modes of action.
Expected Outcomes
A library of novel microbial natural products with agrochemical activity; characterised lead compounds with defined modes of action; joint publications and intellectual property; and a validated pipeline for sustainable agrochemical discovery from Australian biodiversity.
Impact and Significance
Sustainable agrochemicals reduce environmental damage from conventional pesticides, support food security, and open new markets for Australian biotechnology. This partnership with NovoNordisk positions the Biosustainability Hub as a global contributor to next‑generation agricultural solutions.
Keywords
- Microbiome engineering & biodiscovery
- Multi-omics analysis
Development and optimisation of production of Steinernema carpocapsae (entomopathogenic nematodes) in bioreactors (air-lift)
Chief Investigator(s)
Yu Sun, Axayacatl Gonzalez, Esteban Marcellin, Tim McCubbin
Background and Need
Australian agriculture increasingly requires sustainable, effective alternatives to chemical pesticides, yet access to reliable, cost‑competitive biological control agents remains limited. Entomopathogenic nematodes (EPNs) offer strong potential, but large‑scale production is constrained by process inefficiencies, poor scalability, and inconsistent product quality. There is a clear need for robust, fermentation‑based manufacturing platforms that enable domestic production of high‑quality biocontrol agents aligned with modern integrated pest‑management strategies.
Project Aim
To develop a scalable, low‑shear fermentation platform for production of Steinernema carpocapsae, enabling reliable, cost‑effective manufacturing of entomopathogenic nematodes for Australian agriculture.
Approach and Key Activities
The project will develop an air‑lift fermentation process tailored to the biological requirements of EPNs, integrating media optimisation, hydrodynamic modelling, and metabolite analytics. Experimental studies will define optimal growth conditions and identify key parameters influencing yield, viability, and infectivity. Analytical workflows will link metabolite profiles to biological performance, enabling rational optimisation. Process data will establish a scale‑up‑ready design basis, including control strategies and operating windows. Outputs will be translated into SOPs and parameter ranges to support pilot‑scale implementation and future expansion to additional species.
Expected Outcomes
A validated fermentation process for EPN production, including defined operating parameters, optimised media formulations, and infectivity‑linked quality metrics. Additional outputs include scale‑up guidelines, SOPs, and comprehensive datasets supporting external validation. These deliverables will enable pilot production, reduce technical risk, and support cost‑of‑goods modelling and commercial readiness.
Impact and Significance
This project will strengthen Australia’s agricultural resilience by enabling domestic production of sustainable biocontrol agents, reducing reliance on imported or chemical inputs. It supports growers with effective, scalable pest‑management solutions while advancing sovereign biomanufacturing capability. Broader impacts include fostering industry–research collaboration, accelerating SME innovation, and positioning Australia as a leader in biological crop protection and sustainable agriculture.
Keywords
- Bioprocess optimisation
- Bioreactor engineering
- Metabolic modelling
- Multi-omics analysis
- Precision fermentation
- Process scale-up & pilot plant
Bio-based solutions for a sustainable agriculture
Chief Investigator(s)
Gary Schenk, Yasmina Sultanbawa, Robert Henry, Volker Sieber, Bastian Blombach, Karen Sieber
Background and Need
Modern agricultural production relies heavily on synthetic chemicals such as glyphosate, which have detrimental effects on the environment and human health. These solutions are increasingly controversial and unsustainable. There is an urgent societal and environmental need to develop bio‑based agri‑chemicals that combat pathogens such as fungi and insects while reducing greenhouse‑gas emissions and supporting the transition to a zero‑carbon bioeconomy.
Project Aim
This project aims to establish an interdisciplinary platform that integrates biotechnological production of known natural agri‑chemicals with the discovery of new bioactive compounds from plants native to Queensland.
Approach and Key Activities
The strategy employs two synergistic streams: process optimisation for producing the herbicidal carbohydrate 7‑desoxy‑seduheptulose (7dSh) from agricultural waste, and bioprospecting Queensland’s biodiversity for novel secondary metabolites. Key activities include engineering C. glutamicum and cell‑free enzyme cascades to convert sugarcane bagasse into bioactives. In parallel, genomic and chemical screening is being used to identify antimicrobial peptides in native flora. Field trials against fungal pathogens will validate efficacy.
Expected Outcomes
Concrete outputs include optimised enzymes and bacterial strains for high‑yield 7dSh manufacturing. The project will deliver a library of validated small molecules and peptides with herbicidal and antifungal properties. It will also provide a functional bioproduction pilot plant and establish a new intercontinental pipeline for knowledge and material transfer between Queensland and Germany.
Impact and Significance
The agricultural industry benefits from sustainable alternatives that reduce reliance on harmful synthetic chemicals. Society gains through enhanced food security and reduced environmental damage. This initiative also creates economic opportunities for regional and Indigenous communities through co‑designed projects, while establishing a global leadership hub for the emerging bioeconomy.
Keywords
- Bioprocess optimisation
- Cell-free biomanufacturing
- Multi-omics analysis
- Waste valorisation
Discovering new antibiotics targeting gram-negative bacterial cell wall formation
Chief Investigator(s)
Background and Need
Antimicrobial resistance (AMR) is one of the greatest threats to global health, with Gram‑negative bacteria responsible for the majority of drug‑resistant infections. Current antibiotics are failing, and the pipeline of new drugs targeting Gram‑negative pathogens is critically thin. Novel chemical scaffolds that exploit previously unexplored bacterial cell‑wall biosynthesis pathways are urgently needed to address this crisis.
Project Aim
To discover and characterise new antibiotic compounds from Australian soil microbes that selectively inhibit Gram‑negative bacterial cell‑wall formation.
Approach and Key Activities
This project combines advanced genome mining of Australian soil microbial isolates with BLOOM’s integrated MATRIX microbioreactor platform and nitric‑oxide‑mediated transcriptional activation (NOMETA) strategy to unlock previously silent biosynthetic gene clusters. Candidate compounds are isolated and structurally characterised using NMR and mass spectrometry, then evaluated against a panel of drug‑resistant Gram‑negative pathogens in collaboration with IMB. Structure–activity relationships will guide hit‑to‑lead optimisation.
Expected Outcomes
New antibiotic compounds active against drug‑resistant Gram‑negative bacteria; characterised biosynthetic gene clusters; peer‑reviewed publications in high‑impact journals; provisional patents on lead compounds; and a validated platform for accelerated antibiotic biodiscovery from Australian soil microbiomes.
Impact and Significance
AMR already causes more than 700,000 deaths annually worldwide, with projections reaching 10 million by 2050. This project delivers new chemical weapons against drug‑resistant infections, benefiting healthcare systems, patients, and the Australian biotechnology sector. It also positions the Biosustainability Hub as a national leader in antibiotic biodiscovery.
Keywords
- Microbiome engineering & biodiscovery
- Multi-omics analysis
Towards the sustainable discovery and development of new antibiotics
Chief Investigator(s)
Background and Need
Microbial genomes encode a vast arsenal of biosynthetic gene clusters (BGCs) capable of producing novel bioactive compounds — yet most remain silent under standard laboratory conditions, leaving an enormous reservoir of chemical diversity inaccessible. As antimicrobial resistance escalates and demand grows for new agrochemicals and environmental solutions, developing reliable methods to access this hidden chemical space has become one of the most pressing challenges in natural‑product science.
Project Aim
To define how silent biosynthetic genes within microbial genomes can be systematically accessed to unlock new chemical diversity and facilitate the discovery of next‑generation antibiotics, agrochemicals, and environmental defence molecules.
Approach and Key Activities
This Fellowship applies interdisciplinary approaches integrating genome mining and advanced metabolomics to identify, activate, and characterise silent BGCs across diverse Australian microbial isolates. Phylogenetic‑guided prioritisation of the most divergent biosynthetic genes is combined with targeted activation strategies — including NOMETA and simulated stress conditions — to unlock previously inaccessible chemistry. Newly produced metabolites are structurally characterised and evaluated for biological activity across antibiotic, agrochemical, and environmental applications.
Expected Outcomes
Newly defined microbial defence molecules with antibiotic and agrochemical relevance; validated genome‑mining and metabolomics workflows for silent‑BGC activation; more than 15 peer‑reviewed publications; trained next‑generation scientists equipped for research and innovation careers; and strengthened international collaborations across Europe, Asia, and the Americas.
Impact and Significance
This project positions Australia at the forefront of drug discovery by transforming how microbial chemical diversity is accessed and exploited. It delivers new chemical leads for antibiotics and agrochemicals, addresses future needs in environmental science, and builds a stronger Australian research workforce — directly benefiting human health, agricultural productivity, and national innovation capacity.
Keywords
- Microbiome engineering & biodiscovery
- Multi-omics analysis
Light-driven biocatalytic cell factories
Chief Investigator(s)
Gary Schenk, Ben Hankamer
Background and Need
Australia possesses immense solar resources, yet renewable‑fuel production is constrained by the low efficiency of natural photosynthesis, which typically captures only ~1% of incoming photons. Conventional methods lack the economic viability required for commodity‑fuel sectors. Developing high‑efficiency biocatalytic cell factories is essential to capture the projected $12 trillion global green‑hydrogen market. There is an urgent societal need for carbon‑neutral biomanufacturing to ensure economic and environmental security.
Project Aim
This project aims to develop high‑efficiency microalgae cell factories for renewable, solar‑driven hydrogen production and versatile “plug‑and‑play” biocatalysis to power sustainable, carbon‑neutral advanced‑manufacturing industries.
Approach and Key Activities
The strategy employs cutting‑edge synthetic biology and sequential CRISPR engineering to re‑engineer microalgae. Key activities include combining multiple validated gene modifications into single cell lines to maximise electron flow from water to hydrogenase and other enzymes. In parallel, “light‑green” mutants are being engineered to improve light penetration within dense cultures. The project also integrates pilot‑scale trials with advanced techno‑economic and life‑cycle analyses to evaluate the feasibility of scaled‑up hydrogen production and high‑value industrial‑chemical synthesis.
Expected Outcomes
Concrete outputs include stable, self‑propagating algal cell lines with photon‑conversion efficiencies significantly exceeding current limits. The project will deliver a library of engineered mutants, validated multigene CRISPR methods, and comprehensive techno‑economic models. Additional outputs include new patents and high‑impact publications, raising the technology‑readiness level for industrial adoption.
Impact and Significance
The advanced‑manufacturing and energy sectors benefit from cost‑competitive, CO₂‑neutral production methods. Australia gains national fuel security and a leadership position in the global green‑hydrogen market. Regional communities benefit from sustainable job creation, while society benefits from reduced environmental impact through the transition to renewable bio‑industry.
Keywords
- Bioprocess optimisation
- Process scale-up & pilot plant
- Synthetic biology & strain engineering
- Waste valorisation
ARC Research Hub for Engineering Plants to replace fossil carbon
Chief Investigator(s)
Gary Schenk, Karine Chenu, Robert Henry, Ian Godwin, Karen Massel, Karen Aitken
Background and Need
Eliminating greenhouse‑gas emissions requires replacing fossil carbon with renewable sources such as plants. While ground transport can electrify, long‑haul aviation remains dependent on carbon‑based fuels. Current sustainable aviation fuel (SAF) production is limited by insufficient capacity and high costs relative to traditional fuels. Previous efforts using food crops were inefficient, highlighting the urgent need for optimised biomass feedstocks to make renewable energy economically viable.
Project Aim
This project aims to engineer new plant varieties with modified biomass composition and develop matched enzymes to enable cost‑effective, industrial‑scale production of sustainable aviation fuel and renewable chemicals.
Approach and Key Activities
The Hub integrates genomics, gene editing, and mutagenesis to re‑engineer the cell walls of rice, sorghum, and sugarcane. Activities include identifying genetic targets to reduce lignin and increase fermentable glucose, followed by validation through high‑throughput screening. In parallel, the team will engineer novel enzymes specifically optimised to deconstruct the redesigned biomass. A “Feedstocks‑to‑Fuels” pipeline will then demonstrate efficient conversion of the modified plants into dimethylcyclooctane, a high‑performance, drop‑in renewable jet fuel.
Expected Outcomes
The project will deliver optimised plant genotypes with altered biomass composition and high‑efficiency engineered enzymes for industrial use. Key outputs include a robust innovation pipeline for commercial crop varieties, doubling carbon‑conversion rates to achieve price parity with fossil fuels. Validated SAF‑production processes and new intellectual property will support immediate commercial adoption.
Impact and Significance
This program enables carbon‑neutral long‑haul travel, essential for Australia’s international connectivity. It secures domestic fuel supply, enhances national security, and is projected to create more than 7,400 regional jobs by 2030. Agricultural producers benefit from high‑value cropping opportunities in sugarcane and sorghum, while society benefits from a significant reduction in aviation emissions.
Keywords
- Bioprocess optimisation
- Cell-free biomanufacturing
- Precision fermentation
- Process scale-up & pilot plant
- Waste valorisation