New Zealand Institute for Bioeconomy Science funded Research Programmes

Traditional production systems for agri-foods are undergoing transformation. They are challenged by climate change, shifting consumer attitudes and preferences, and technology unlocking new opportunities. Alternative ways of producing food ingredients are sought that are efficient, adaptable, and pitched towards environmental, animal welfare, or nutritional benefits.

NZ can participate and benefit during this transition by implementing legislative, scientific and infrastructure solutions. To maintain our enviable reputation as an agri-food exporter, innovations and new industries must be blended with deep knowledge of land-based agriculture.

To this end, and in collaboration with industry partners, we are creating an efficient, low-emissions process for Precision Fermentation (PF). This will deliver bespoke, high value ingredients that can substitute or complement those from traditional animal sources. Process operations are tailored to the NZ context, in particular leveraging abundant and underutilised side streams recovered from primary industry. This research programme is a novel approach to enriching high-technology trade within the circular bioeconomy.

PF uses directly modified microorganisms such as yeast and bacteria to convert simple carbohydrates into specific desirable molecules. The microbes are grown on sugary fermentation feedstock generated from recovered bioresources such as pine wood chips or pulp. The outputs are then harvested and purified. As a byproduct, single cell biomass is produced for spinoff as a high protein animal feed.

This PF programme generates scientific and economic advantage from the impending modernisation of NZ’s regulatory position on genetic engineering. It provides the foundation for a diverse new sector equipped with disruptive science and technologies, such as synthetic biology. NZ can position itself as a key player in the modern global food ecosystem, contributing to better wellbeing for people and planet through innovative food and nutrition solutions.

Innovations that have enabled NZ to transport high-value food large distances to key markets are the foundation of our strong export sector. NZ’s lucrative fresh-fruit industry is dominated by gold and green kiwifruit and apples, accounting for NZ$3.5 billion of export earnings for NZ per year. These fruit can be harvested in NZ, stored and transported in ships across the world over 6 months and still be delicious on arrival in northern hemisphere markets. Most of NZ’s other fresh fruit crops (e.g. summer fruit and berry fruit) are limited to domestic and very near markets because they do not have sufficient storage life to allow transport in bulk by sea-freight to distant markets, such as Asia and Europe.

The aim of this research programme is to replicate the outstanding storage capacity found in kiwifruit in other fast-perishable fruits. This will enable NZ to grow and expand its horticultural crops to reach its ambitious goal of increasing its horticultural export value from NZ$7 billion to NZ$12 billion per year. More and different types of export-fruit will be grown in other regions in NZ, spreading economic benefits, and adding up to $1B to the local economy. It will directly benefit growers through increased returns and more flexible harvest windows. Diversification will reduce impacts from extreme local weather events, reduce food waste and lower NZ’s carbon footprint by replacing air-freight with sea-freight.

Fish cells cultured in the lab can be used in several ways. One of these is as fish cell production systems (FCPS) for making new products. This technology has the potential to change the way we produce seafood and generate marine products (e.g. collagen) through a technology known as cellular agriculture (CellAg). Cells and the media they are cultured in are the bricks and mortar of this technology; cells must be viable, healthy, multiply rapidly, and be able to grow in large numbers. Media must be defined, animal-free, and preferably sustainably produced.

Existing fish cell lines and media do not meet these requirements, resulting in unstable foundations for seafood CellAg. Consequently, the technology is not commercially viable; there are no CellAg seafood products available globally. Our programme will expand knowledge of fish-cell culture, generating an in-depth understanding of cultured cells nutritional/environmental needs leading to enhanced isolation and proliferation which underpins CellAg technology. Once we understand fish cells’ optimal culture requirements, we can develop suitable natural nutrient sources. We will apply this knowledge to explore two CellAg use scenarios: cell-derived collagen and cell-based fish meat.

This programme also seeks to generate an understanding of the cultural/social aspects associated with acceptance of FCPS. This includes understanding Māori perspectives and concerns about products made for cells (e.g. sustainably produced media), by cells (e.g. collagen), and from cells (e.g. seafood), particularly in relation to taonga species.

This programme will fundamentally change the way we utilise cultured fish cells, accelerating progress in cultured seafood, and unlocking new avenues for their use in novel products. In doing so we will place NZ at the technological forefront in cell line development and media formulation.

Crops grown on arable land are an abundant resource and already provide most of the calories in people’s diets. Consumers are increasingly looking to these plants to do much more – to meet a wider range of culinary and nutritional needs, and to help address global concerns around sustainable ecosystems and animal welfare.

Food manufacturers have been quick to respond with many novel products. However, these are often highly refined and stripped of their whole-food benefits, have poor taste and texture, carry high sodium content, and can have hidden damage to essential amino acids. The next generation of plant-based foods will need to be prepared more sensibly with gentler handling of the inherently healthy raw materials and better guardianship of environmental impact.

New Zealand can participate in this opportunity by developing the science and technologies to produce unique highly functional plant foods. Our research programme will design models of crop fractionation processes that incorporate eco-sensitivity, value chain dynamics and circular bioeconomy, while maximising ingredient techno-functionality and health benefits. We will test at pilot scale how a new industry could operate by using exemplar crops known to grow well locally, like green peas, oats and hemp.

We have gathered some of the brightest minds in process engineering, food science, sustainability evaluation, economic analysis and human nutrition. The team also includes many industry partners, from plant breeders, growers and processors to ingredient-users and food manufacturers.

Our aim is to support the arable crop processors of Aotearoa. We want to inspire entrepreneurs in the emerging proteins sector to become successful international suppliers of high-value plant-based food ingredients. In this way our land-based industries can continue to transition towards a profitable low-emissions future.

In New Zealand, and globally, there is a gap in biosecurity defences. This gap allows aerial invaders-invasive pests (insects and pathogens) to reach New Zealand via the wind-assisted pathway; they can spread within New Zealand via this pathway, irrespective of their arrival mode. There are no effective tools to manage this pathway of pest movement, leaving a hole in our biosecurity net. This hole will widen as climate change brings extreme weather events able to transport aerial invaders to our shores, and as the habitat ranges of these invaders expand - both in their source regions and in New Zealand.

It is time to tighten our biosecurity net and close the aerial invader hole.

Our diverse science team will develop a novel, integrated Aerobiological Surveillance and Prediction System (ASaP) to close the aerial invader hole in our biosecurity net. ASaP integrates internationally new science on:

• long-distance atmospheric dispersion modelling
• atmospheric boundary-layer dynamics
• rainfall washout/survival by flying insects.

We also extend existing knowledge on pathogen atmospheric-transit survival, and include innovative aerial invader surveillance by our Māori Partners Taranaki Mounga on the Taranaki coast.

Our science was co-developed with our Programme Advisory Committee, representing the entire biosecurity chain. ASaP will be used by MPI to optimise existing biosecurity systems aligning to Pre-border, Border and Post-Border surveillance and risk analysis biosecurity activities.

Over the past decade, NZ has battled multiple aerial invaders, which are now established pests (for example, myrtle rust, fall armyworm) and there are more on our doorstep, circulating in Australia/Asia-Pacific. Preventing establishment of just 1 serious pest would recover programme costs 10 to 100 times (NZ$0.125B to 1.25B) through avoided losses in the forestry and/or horticultural sectors, maintenance of carbon sequestration, and through biodiversity conservation.

Action to help New Zealand meet its net zero carbon emissions target by 2050 has a current focus on the establishment of new forests. We propose that the targeted integration of isolated or small clusters of trees into low to mid-sloping grasslands will provide an alternative to large-scale conversion to exotic forests, with substantial economic increases in carbon credits and additional co-benefits for animal fodder and shelter, reduced erosion, increasing farm resilience to climate extremes, increased visual amenity, and the enabling of kaitiakitanga. We aim to test that this approach will lead to increases in biomass and soil carbon stocks that exceed those for the same ground area of continuous forestry, contributing significantly to low-emissions and climate-resilient agricultural practices.

For the first time we will quantify the enhanced biomass and soil carbon stocks associated with edge effects at tree/grassland boundaries in hill country widespread in rural New Zealand. Across these boundaries we will determine the soil microbial mechanisms regulating decomposition and stabilisation of soil carbon using key soil properties and next-generation DNA metagenomics. We will then develop and validate microbially explicit ecosystem models to predict changes in carbon stocks at site scale. From this we will undertake quantitative scenario modelling, incorporating decision constraints by land managers, to predict the economic, environmental and cultural value of increased carbon stocks at landscape scale and recommend the optimal spatial establishment of tree clusters for benefits and their value across nature’s contribution to people.

Our research will strengthen the country’s international reputation for action to mitigate and adapt to climate change, support landowners including Māori to deliver sustainable land management, enabling kaitiakitanga, well-being, and the prosperity of the rural sector.

Worldwide, current widely used vertebrate pest control toxins are harmful to humans and non-target animals. Therefore, their use is being increasingly restricted or banned. There is a consequent growing global demand for safer, more selective toxins.

We will develop selective toxins for high-precision, environmentally sound vertebrate pest control using cutting-edge science to invent new types of toxins that exploit physiological and metabolic differences between species.

Our new products will help protect our environment by enhancing pest management, improve sustainability and productivity of our primary industries, and support Predator Free 2050 to achieve its aspirational goals. Within this programme, hapū/iwi will explore how Māori values inform their own policy positions about toxin use in te taiao.

Our research will provide a new toxin manufacturing industry for Aotearoa New Zealand with potential to target global markets. This represents a significant economic opportunity for Aotearoa New Zealand, as we have the knowledge and reputation that give us a head start. We are the only team in the world seeking to develop toxin discovery technologies that target individual pest species. Our discovery research will develop new candidate toxins for mice, possums and stoats, which are significant threats to our native flora and fauna.

Our ambitious research programme brings together New Zealand’s best researchers in the field from the University of Auckland, Victoria University Wellington, and Manaaki Whenua – Landcare Research, supported by an international group of leading academics, and commercial, industrial and regulatory experts.

Extreme wildfire is accelerating much faster than predicted—research and operations worldwide are struggling to keep ahead of the fire-front. Even in NZ, what was once rare is now the norm. The changing climate is increasing the frequency and severity of wildfires, and escalating the risks, especially for those living within the Rural-Urban Interface (RUI, Lake Ōhau is a tragic example). We have no wildfire code—decisions made today will constrain homeowners’ options for decades. Our indigenous forests, once

considered “safe” from fire, are under threat. Today, the annual average direct impact of rural fire on NZ’s economy is ~$140M, with indirect ‘costs’ estimated to be at least 2-3 times the direct cost, plus indirect impacts as much as 30-60 times direct costs. The direct costs alone are predicted to rise to ~$550M/annum by 2050 under a likely climate- change scenario. A world-class international team from Scion, US Forest Service Missoula Fire Science Laboratory, San Jose State University, US Forest Service Pacific Northwest Laboratory, Karlsruhe Institute of Technology, RMIT, USFS-Colorado, Canterbury and Lincoln University, will challenge existing understanding of the transitions between linear (predictable) and extreme (unpredictable) fire, especially in relation to fuels. Predicting the physical processes driving fire-spread is central to all fire readiness; without that knowledge, it is not possible to develop effective tools and strategies to keep firefighters and communities safe. We address the Government’s investment priorities for the environment by enabling NZ to better manage the impacts of fire. All rural fire stakeholders will benefit from this programme, including Fire and Emergency NZ (FENZ) Department of Conservation (DoC), rural landowners, RUI residents, and in particular Māori with their role as kaitiaki of our indigenous forests.

Aotearoa-New Zealand (A-NZ) has ambitious environmental goals, and the commitment to these has been reaffirmed in A-NZ’s COVID-19 economic recovery priorities. The primary sector underpins A-NZs economy and land managers are integral to achieving these environmental goals and leading A-NZ through its economic recovery.

However, many land managers are not achieving the scale of action necessary to improve environmental performance. Conversely, they are ‘overwhelmed’ by the complex issues they face. Our research will address this issue and provide the systemic changes needed to enable land managers to act, which will improve farm environmental performance, ecosystem function and biodiversity, farm financial viability, national economic performance, rural mental health, and environmental, economic, and social resilience in the face of disruptors such as COVID-19 and climate change.

Past research has often assumed the problem is an ‘information deficit’ and focused on understanding and influencing ‘leading’ or ‘trailing’ land managers. In contrast, our research focuses on the middle cohort of land managers who are willing to make necessary changes but are constrained by the multiple systems (finance, policy, social, market, etc.) that affect how they shape their decisions and actions.

Our social science research examines, innovates, and tests system leverage points that will enable the middle cohort of ‘overwhelmed’ land managers to respond proactively to the environmental, market, and societal challenges they face. We partner with Crown Research Institutes, universities, government, and industry to research the agency of land managers, the systems affecting them, and the influence of (a) public and private narratives; (b) debt loading and investment practices; (c) policy signals and perceptions; and (d) traditional and new agents of change in empowering rural land managers to respond proactively.

Planted forests are an essential component of New Zealand’s transition to a carbon-neutral bio-economy. However, our ability to grow radiata pine and other species successfully is at risk due to uncertainty around our changing climate.

One approach to ensuring our planted forests remain productive is to use a tree’s phenotype (characteristics), which is a product of the interaction between genetics and the environment, to identify trees that grow particularly well in specific environments.

Work identifying trees with outstanding phenotypes has already begun, but there is a lot more to be learned about our planted forests. New ways of collecting and analysing data about tree volume, height, shape, carbon content and form – that consider trees in three dimensions – will enable us to identify exceptional trees rapidly.

This research programme is focussed on delivering high throughput forest phenotyping using remotely sensed data and advanced concepts in data science. Combined with genomic data, we will be able to select and breed trees with desirable traits such as high carbon storage and resistance to disease and drought exacerbated by our changing climate.

The programme also extends to indigenous forests, with the aim of combining data with mātauranga Māori to explore the cultural linkages Māori have to forests and taonga species. This “cultural phenotyping” is expected to lead to modern applications of traditional forest-based economic opportunities including diverse forests capable of

delivering a wider range of benefits and to the reinvigoration of Māori customary practices.

Forest-scale phenotyping of millions of trees will enable forest growers to optimally site different genotypes under current and future climates, increasing plantation productivity, health and resilience and contributing to economic, environmental and social gains.

Our research will use te ao Māori worldview and whakapapa frameworks alongside the integration of value and ecological networks to re-imagine biocultural solutions that simultaneously restore ecological systems, reinforce identity, reconnect people to place, enhance community wellbeing, and deliver sustainable economic growth for communities. We will embed our research within Iwi-specific cultural learning institutions which will support the training and development of new kaitiaki and tangata tiaki.

Our research will be embedded within four case studies: (1) Sequences of wetland plant communities that support mahinga kai aspirations, led by Awarua Rūnaka, (2) Breaking arrested forest succession through economic development, led by Tūhoe Tuawhenua, (3) Biocultural regeneration of Moehau, led by Pare Hauraki, and (4) Tītī by-products and weka management enhance biodiversity and community wellbeing, led by Rakiura Māori.

We will use both te ao Māori and scientific knowledge systems to develop whakapapa frameworks and social-ecological networks and test how the impacts of kaitiakitanga interventions and economic activities cascade through ecosystems and our human communities. To facilitate this process, we will leverage new and existing data sets and network theory to explore the myriad of connections between human values, practices, and metaphysical and biophysical elements in ways that can be used in decision-making and cultural impact assessments.

We will then determine how individual components and the entire architecture of studied social-ecological systems relate to well-being outcomes. The Iwi-entities use this information to achieve outcomes related to restoring biodiversity, promoting sustainable business ventures, improve community wellbeing, and reconnect people with their lands and seas.

New Zealand’s plant-based economy relies heavily on temperate conditions to deliver high quality fruit, vegetable and forestry products to local and global markets. These plants are being affected by the climate crisis due to warming climate, loss of cold nights, as well as extreme weather events such as heatwaves. Flowering is a key parameter for New Zealand’s horticultural and forestry industries, determining yield and quality of its products. Heat reduces flowering in temperate perennials, thus the climate crisis is beginning to threaten horticultural sustainability as New Zealand experiences warmer temperatures.

Our research team is world leading in their study of flowering and the genes that control plant response to the environment. This research programme will use kiwifruit, pine and other plant models as research tools to study flowering. New knowledge will be used to generate variants in commercial crops and to develop ‘climate-ready’ cultivars. This will enhance the country’s fastest growing sector, and protect its competitive advantage as a supplier of premium plant products.

Through our new exemplar plants with increased flowering, we will engage the public in discussion around how climate change may affect New Zealand’s crops as well as how new genetic technologies are one tool to address these issues. The programme will also co-develop new strategies for plant breeding with Māori partners that integrate indigenous knowledge with new selective breeding methods and gene technologies. Public engagement will be a key part of the project, identifying and developing ways for the New Zealand public to positively engage with the scientific concepts.

Wilding conifers are an economic and environmental disaster that already cover 1.5M of NZ, including Māori land. A further 7.5M ha of productive or iconic conservation land are threatened by invasion in the next 30 years. In response, the Government established a National Wilding Conifer Control Programme to deal with this serious and growing problem. Existing populations are being treated but current control efforts do not consider that cleared land is more likely to be re-invaded due to incomplete initial control, soil legacy effects, seed banks and other causes. We must develop effective strategies to create long-term resistance to re-invasion on treated land – Vive la résistance!

Re-invasion processes differ significantly from those of initial invasion and a critical international knowledge gap exists on how various factors interact to drive re-invasion. We will disentangle the multiple drivers of re-invasion to overcome this gap and address the devastating problem of wilding-conifer re-invasion in NZ. The outcomes of this programme will transform current wilding-management practices by breaking an otherwise inevitable cycle of treatment/re-invasion/re-treatment.

Benefits to NZ from this research include securing $6.3B of projected benefits by 2050 from the current > $100M investment in wilding control and generating substantial benefits of ~$750M (benefit-to-cost ratio ~54:1) by reducing treatment costs and by avoiding multiple re-treatments. Increasing participation of Iwi/Māori in management of wilding re-invasions and restoring Māoritanga and landscape aesthetics are also key research outcomes.

We typically think of seafood as delicious shellfish and fillets, but the enormous range of harvested animals from Aotearoa’s aquaculture and fisheries also represents a complex mixture of molecules with uses far beyond food. Many of these molecules have special properties making them valuable commercially, including as products for human/animal health. They range from big structural proteins for biomedical scaffolds, through to anti-inflammatory omega-3s, and blood pressure-lowering or anti-aging peptides. The good news is that these molecules are often found in by-products and by-catch, so we can grow our seafood industry without affecting seafood availability, or needing more fish to be caught - a genuine vision of kaitiakitanga. The challenge is how to extract them all out of really diverse marine organisms, containing different types and combinations of the molecules. Current technology can’t do this. We need new technology that is economical, uses environmentally friendly processes with low emissions and the biggest challenge, doesn’t destroy one component while recovering another.

We need factories that can change how they operate to match raw materials with the products we want. Right now, we can assess composition using chemical testing, but this takes a long time. For our responsive factories to work, we need analysis in real time as material arrives or changes. The Cyber-Marine research programme will develop AI-integrated sensor systems able to immediately tell us what’s in the raw material, then use the information to direct optimised processing. This will require development of new low-energy extraction technologies that use the differences in properties of molecules to sequentially separate the components.

While this programme centres on seafood, the technology will have application across the primary-production sectors and beyond.

Our future wellbeing and fate of our trees and forests are inextricably intertwined. However, survival of many of our cornerstone native and commercial tree species is at serious risk due to rapidly changing environmental conditions. Breeding new tree varieties tolerant to future conditions will take too long and, for most species, we do not know if climate or disease tolerance traits are even present in their genomes. In short, time is running out to future-proof our trees and forests, putting their survival, and our quality of life, at risk.

We aim to make our trees and forests more adaptable to disruption by using their microbial associations. Just like humans, trees live in close association with diverse microorganisms. And, just like humans, microbes living on plants can profoundly impact their health and fitness. For example, the microbes living in the human gut not only affect our physical state, but communicate directly with our brain, and are associated with psychiatric and neurologic disorders. We contend the soil-root-microbiome has the same function for trees as the gut-microbiome has for humans. We will use the root-microbiome to alter plants environmental perception, learning, and responses to changing environmental conditions.

To achieve these outcomes, we will develop the first tree-microbiome model system using radiata pine. We use pine as we have a wealth of physiologic, trait, and genetic information, availability of national and international trial networks, and access to co-evolutionary host-microbiome associations across its natural and globally expanded ranges.

Our expert national and international team will unravel how the root-microbiome functions to enable extended tree phenotypes that can resist climate change. This is a transformational opportunity to climate-proof both our native and plated trees and forests.