The Cawthron Institute Trust Board Smart Ideas funded projects

Aotearoa New Zealand’s aquaculture sector urgently needs new, practical strategies that boost production performance and improve climate change resilience and robustness for current and future challenging farming environments. Mitochondria, “powerhouses” of the cell, are crucial for organism metabolism and temperature sensitivity. They are a universal target that can be harnessed to improve performance and efficiently overcome these fundamental challenges. Mitochondrial-targeted therapies are increasingly used in medicine to treat diseases, like diabetes, cardiovascular disorders, and cancers. Similar approaches have recently been applied overseas in livestock industries through breeding, nutrition, and exercise to improve performance, but the potential of enhancing mitochondrial function in aquaculture species remains untapped. Our research fills this gap by demonstrating how mitochondrial function influences performance, resilience, and robustness in farmed aquatic species of Aotearoa New Zealand. Using specialised respirometry and spectrometry equipment, we will measure mitochondrial function in key tissues of commercially, culturally, and ecologically important aquatic species (e.g., salmon, snapper and shellfish). Tested individuals will have different performance levels, genetic, nutritional, and environmental backgrounds. With this metabolic knowledge we will identify actionable strategies (e.g., improved diets and breeding) to boost mitochondrial function that industry can immediately apply to improve the performance and survival of commercial stocks under rapidly changing environments due to climate change. Our team includes experts in mitochondrial physiology, animal breeding, genomics, and aquaculture from leading Aotearoa New Zealand research organisations (UoAuckland, Plant and Food Research, AgResearch, and the Cawthron Institute), alongside international collaborators from Australia and Europe. Together with industry partners and iwi stakeholders, we will ensure our findings translate into commercial practice. Our research will demonstrate how mitochondrial-enhanced organism performance can address key challenges including climate change across food production sectors beyond aquaculture.

The global agriculture industry is still reliant on synthetic nitrogen fertiliser (N-fertiliser) produced using natural gas, which currently accounts for 1% of global greenhouse gas emissions. Aotearoa New Zealand’s agricultural and horticultural sectors currently release the equivalent of over 900,000 tonnes of CO2 per year through N-fertiliser production. Reaching our national 2050 net-zero greenhouse gas emissions target, while maintaining our agricultural and horticultural economies, will require technological innovations that shift the sector to more sustainable practices.

Our solution to enable these sectors to transition away from synthetic N-fertiliser, uses microscopic organisms called cyanobacteria. Some cyanobacteria can take nitrogen from the air (atmospheric nitrogen or N2) and convert it into nitrogen forms that plants can use such as ammonia (NH3) and nitrate (NO3). Because cyanobacteria consume CO2 through photosynthesis, this could provide a climate-positive and sustainable nitrogen source for agriculture and horticulture.

However, the typically low nitrogen-fixation rates of cyanobacteria are currently a barrier to progress. Our researchers plan to overcome this challenge by implementing improvement strategies that increase the nitrogen-fixation capacity of cyanobacteria through biotechnological interventions and manipulation of growth conditions. The resulting increases in nitrogen-fixation levels could create opportunities for industrial-scale production of cyanobacterial N-fertiliser and move the fertiliser industry away from their dependency on fossil fuels.

Additional benefits from cyanobacterial N-fertilisers could include point-source CO2 capture opportunities, reduced nitrous oxide emissions, less nitrogen run-off into waterways, improved soil health with increased resilience to extreme rain events and drought, better N-fertiliser price stability and lower fertiliser transportation costs.

Climate-positive and environmentally sustainable solutions, such as this, will ensure that our agricultural and horticultural sectors can maintain favourable market access with premium pricing – while also meeting impending climate change obligations.

The New Zealand salmon farming industry, currently valued at $320M, is already economically significant for many rural areas and is expected to grow markedly with approved expansions both onshore and into the open ocean. However, the diets fed to our Chinook salmon, sourced and formulated overseas from research on different salmonid species (Atlantic salmon and trout), are not optimised for Chinook salmon or our local conditions. This results in poor feed efficiency, requiring more feed for less growth in fish fillet. Such inefficiencies lead to metabolic imbalances and excessive fat deposits around internal organs, adversely affecting fish health. Consequently, optimizing diet formulations has become a critical priority for the industry to enhance fish health and improve feed conversion.

This project aims to transform salmon diets by adopting a radical approach based on the protein leverage theory, a concept developed by our collaborators, David Raubenheimer and Stephen Simpson from the seminal work on locusts at the University of Oxford. This faster, more precise approach uses nutritional geometry to balance proteins, fats, and carbohydrates to meet the specific needs and appetites of salmon, surpassing the slow progress of traditional nutritional approaches. We are working with leading fish nutritionists, fish health and diet design researchers from New Zealand and Australia, to comprehensively understand and define the dietary requirements of our Chinook salmon.

For the first time, we will pinpoint the exact nutritional needs of our prized Chinook salmon, empowering New Zealand's salmon producers to lead the charge for change. The benefits extend far beyond the fish farms – healthier diets mean healthier fish and a cleaner environment- while providing one of the healthiest animal proteins for consumers.

Lake ecosystems have suffered widespread degradation due to human activities which has led to a loss of vital ecosystem services such as climate regulation, recreation and tourism opportunities, fisheries, drinking water supply, and biodiversity. As environments change organisms respond by altering the functional genes present in the community. By looking at the DNA, we see what genes are present and in particular, identify those with a role in coping with environmental challenge or indicating stress. Building on the work already completed in this project, the proposed extension will focus on developing rapid, cost-efficient gene-based detection methods to identify the key stressors driving ecological decline in lakes. 

This innovative research has a high potential to benefit the environment by allowing better decisions for the management of freshwater ecosystems. The research also supports national policy which requires better management of New Zealand’s freshwater and to work towards achieving Te Mana o te Wai.

Lakes in Aotearoa-New Zealand are in crisis, with recent research showing that approximately 45% are in poor health. This poor health is directly linked to human-induced factors including nutrient and sediment run off, chemical pollutants, habitat modification and the non-native species introductions. With resources to restore and prevent further decline being limited, it is essential efforts are effectively targeted. However, current methods for assessing lake health are time-consuming, costly, and often only focus on water quality without an understanding of the wider lake system.

This project will enhance lake restoration by developing a DNA-based approach to rapidly identify the most harmful impacts while also detecting culturally significant organisms. Our new approach targets the lake sediments. All inputs into lakes and the DNA from organisms living in lakes eventually sink and combine to form sediment on the lakebed. Using cutting-edge molecular techniques, we will explore not only what lives in a lake but also how these organisms are functioning. This information will provide new insights into the pressures impacting a lake and will help guide effective lake restoration.

Our vision is to support better lake restoration outcomes by making it easy for the people to identify the causes of lake degradation with limited sampling and analysis effort. We want to create a user-friendly dashboard that distils complex data into helpful and practical insights that guide restoration, protection and management efforts. Our new approach will be developed in partnership with iwi and regional councils and central government to ensure it if fit-for-purpose. This new tool will position Aotearoa-New Zealand as a global leader in lake management and restoration and will support the reversal of our current lake health crisis.

Shellfish aquaculture production is rapidly growing worldwide and has been identified as one of the most environmentally sustainable sources of animal protein. Infectious diseases cost the global aquaculture industry more than NZ$10 billion every year and affect livelihoods. Climate change exacerbates disease outbreaks which are becoming more frequent and intense, constraining the expansion of shellfish production worldwide. A striking example is the Pacific oyster mortality syndrome driven by a virus that devastated the industry globally, including New Zealand, where production was halved in 2010. With no therapeutic treatments, the shellfish industry relies on selective breeding to mitigate disease. Despite being effective this approach may be slow to implement and hard to access. Recent research breakthroughs reveal the shellfish immune system can provide memory, opening the door to vaccination, previously thought to be impossible in shellfish. 

Using the Pacific oyster and its virus as models, we are developing a scalable and cost-effective vaccine technology to protect shellfish against diseases. We examined the efficacy of a range of vaccines, and administration routes on key life stages. One treatment offered full protection against OsHV1 infection in oyster spat and is now investigated for its transgenerational protection. Co-designed with end-users, the experimental approach will test the best candidate vaccines in the lab and be implemented rapidly under “real life” conditions on farms. Furthermore, thermal priming of oysters’ early life stages will be investigated to promote lasting resistance to pathogens and stressors.

Transferable to other species, the proposed technology will

1.  improve economic and social outcomes for NZ’s aquaculture industry, 
2. open new perspectives for disease mitigation strategies to global shellfish aquaculture, and
3. greatly improve NZ preparedness for the next disease outbreak.

Shellfish aquaculture production is rapidly growing worldwide and has been identified as one of the most environmentally sustainable sources of animal protein. Infectious diseases cost the global aquaculture industry more than NZ$10 billion every year and affect livelihoods. Climate change exacerbates disease outbreaks which are becoming more frequent and intense, constraining the expansion of shellfish production worldwide. A striking example is the Pacific oyster mortality syndrome driven by a virus that devastated the Pacific oyster industry globally, including in New Zealand where production was halved in 2010. With no therapeutic treatments the shellfish industry relies on selective breeding to mitigate disease. Despite being effective this approach may be slow to implement and hard to access. Recent research breakthroughs reveal the shellfish immune system can provide memory, opening the door to the use of vaccination, previously thought not to be possible in shellfish.

We will develop a vaccine to protect shellfish against diseases. Using the Pacific oyster and its virus as a model, we will propose a safe and cost-effective technology to protect young Pacific oysters on farms. The vaccine will be prepared using the classical protocol of virus inactivation. The research will examine the efficacy of a range of vaccines, administration routes, and immunisation on different oyster life stages will be performed. Co-designed with end-users, the experimental approach will test the best candidate vaccines in the lab and will be implemented rapidly under 'real life' conditions on farms.

Transferable to other species, the proposed technology will:

1. improve economic and social outcomes for NZ’s oyster aquaculture industry
2. open new perspectives for disease mitigation strategies to global shellfish aquaculture
3. greatly improve NZ preparedness for the next disease outbreak.

The mining of phosphorus to produce fertiliser depletes geostrategic reserves and costs economies relying on its importation for agriculture billions. Phosphorus must continuously be added to soils as it is lost in the food chain or via leaching in waterways. When phosphorus discharges to aquatic environments, it can cause excess microalgae growth. This project offers an innovative, nature-based solution to phosphorus supply, loss, and pollution — using the same microalgae that cause eutrophication to capture, recycle, and transform phosphorus into valuable, multi-use polyphosphates (polyPs).

Science Leader Dr Maxence Plouviez and his team greatly improved our understanding of the mechanisms behind polyPs syntheses in microalgae, which proteins are involved and how they work. This new knowledge has been essential to develop innovative technologies that recover phosphorus from aquatic ecosystems and ultimately uncover new end-use opportunities for microalgal biomass. A pilot system has been designed and will be tested under real-world conditions at the Earth Sciences New Zealand (ESNZ) microalgae-based wastewater treatment facility in Hamilton. We will now take our real-world production trials to the next level to confirm they are reproducible, and we will also test a different method for bulk production of high-value polyPs in microalgae. Finally, we will establish the potential of spectral technology to monitor the high-value polyPs compounds in microalgae.

The mining of phosphorus to produce fertiliser simultaneously depletes geostrategic reserves and costs billions to the economies relying on its import for agriculture. In addition, phosphorus must continuously be added to soils as it is lost via leaching and in the food chain. Phosphorus discharge causes excess microalgae growth in many aquatic environments. We propose an innovative and environmentally-friendly solution: using the same microalgae that causes eutrophication to recover and recycle phosphorus as high-value polyphosphates.

Dr Plouviez (Massey University) and his group have recently achieved considerable advances in understanding which genes are involved in polyphosphate synthesis in microalgae. These genes are involved in coding the enzymes that catalyse the conversion of phosphate into polyphosphate, however we still know very little about the enzymes themselves. This proposal will take advantage of our collaborations bridging knowledge on the genetics of polyphosphate and the expertise in molecular biology and biochemistry, to investigate the polyphosphate-related enzymes and their structural differences in microalgae specialised for different ecological niches. We will incorporate this new knowledge into innovative technologies that recover phosphorus from aquatic ecosystems, testing them under real-world conditions at the internationally-renowned NIWA microalgae-based wastewater treatment facility.

Climate change is driving more frequent harmful algal blooms, which produce potent toxins that accumulate in freshwater and marine environments. These events pose serious risks to shellfish aquaculture and community health. Current testing methods are expensive, slow, and require specialised laboratory infrastructure, making them inaccessible to many communities, including Māori and Pacific Island groups who traditionally harvest kaimoana. Improving the speed, cost, and accessibility of toxin testing is essential.

We are developing a new biosensor-based testing kit, similar to a lateral-flow test, that uses aptamers (synthetic molecules that bind toxins with high specificity) and a smartphone device for readout. This will enable simple, affordable, field-based testing, empowering communities to monitor seafood safety directly.

To expand the platform’s capability, we are developing aptamers using novel nucleic acid chemistries (XNA), which may improve sensitivity and stability. We are also exploring aptamers for different toxin analogues and selection methods that enhance sensor performance. These innovations will strengthen the platform’s adaptability to diverse environmental conditions and toxin profiles.

Alongside aptamer development, we are working with the University of Auckland to test the sensor with real shellfish extracts, investigate simple sample preparation methods suitable for field use, and transition the system from lab-based setups to portable, low-cost formats.

This work will support community-led monitoring, enable rapid responses to toxin events, and reduce health and economic impacts. It also opens pathways for remote sensing applications, such as buoy-mounted toxin detectors near aquaculture farms, and broader use in food, water, and environmental safety monitoring.

Climate change is driving more frequent harmful algal blooms. These events produce dangerous toxins that accumulate in freshwater and marine environments, adversely affecting shellfish aquaculture industries and community health. Current testing strategies are primarily restricted to industry, as they are expensive and require specialised processing, expertise, and equipment only available in modern laboratories. Places where the infrastructure for such testing is unavailable, for example in many Pacific Islands and Māori communities that traditionally harvest seafood, are most at risk. Sampling frequency, speed, and cost are areas for improvement in food-toxin testing.

We propose to develop a new kind of testing kit that uses biosensor technology (similar to lateral-flow tests) to detect the presence of toxins using a smartphone device. This approach would make seafood safety testing in the field simple and affordable, empowering a wider range of people to become involved in protecting their communities.

These developments will allow community groups, industry, and environmental agencies to increase testing capacity, especially where access to current testing methods is limited, and rapidly respond to toxin events, to avoid adverse health and economic impacts. Additionally, our work expands food testing beyond what is currently possible. For example, it could enable development of remote monitoring instruments for toxin levels in the sea, to be deployed on floating buoys near aquaculture farms to provide real-time data. Additional options include more affordable testing instruments with higher capacity, for Regional Councils and MPI, not only for marine algal-toxins but also for algal and cyanobacterial toxin testing in food, drinking water and recreational waterways. This will transform safeguarding the rapidly-expanding aquaculture industry as well as gatherers of kaimoana and mahinga kai throughout our coastlines and waterways.

Contact jack.hervey@cawthron.org.nz

Estuaries are dynamic mixing zones between rivers and the ocean supporting some of the most productive ecosystems on Earth. New Zealand has more than 400 estuaries along its coastline, and they are enormously valuable to our economy, environment, and society. However, in New Zealand and worldwide, estuary health is declining at an alarming rate. Estuaries face many environmental threats, ranging from pollution to climate change, and these can combine to create catastrophic tipping points from which it is very difficult to recover.

Current efforts to protect and restore estuaries are failing because we haven’t fully understood how these tipping points are triggered or had monitoring tools that can detect signs of declining estuary health early enough to intervene.

In our project, we will examine whether microbes (e.g., bacteria, microscopic algae) can be used to develop tools that transform the way we monitor our estuaries. Microbes underpin estuary health and preliminary studies have shown that they are sensitive enough to detect subtle changes in ecosystem health, enabling early warning of approaching tipping points.

Many organisations in New Zealand would like to use these tools. However, the tools alone would not enable the kind of transformation in estuary monitoring that we need. We will develop a world-leading holistic framework for estuary monitoring that combines microbial tools with mātauranga Māori and conventional estuary monitoring data to harness the benefits of each approach. This information will be translated into management actions that will have a significant impact on estuary health.

Our project will place Aotearoa New Zealand at the forefront of coastal indicator development worldwide and lead to a step-change in estuary biomonitoring that will enable targeted management before irreversible environmental damage occurs.