Author Archive

Interactions between bacteria and phages

Tuesday, November 28th, 2023

Phage force unleashed: Sarah de Roode and Dr Nils Birkholz from the University of Otago exploring the fascinating world of bacteriophages and their potential for disease management.

There are viruses out there, called bacteriophages or just phages, which specifically target bacteria. Nils is interested in the interactions between bacteria and phages, especially how bacteria protect themselves against these intruders. If researchers understand how bacteria defend themselves against phages and what the phage response to this defence is, this fundamental knowledge could contribute to the development of treatments for human or plant diseases.

Bacterial immunity is mediated by different defence systems, each of which is made up of one or more proteins that function in a specific way. For example, many of these proteins cut the DNA of an invading phage into pieces, thereby hindering it from replicating.

How exactly this is achieved can vary drastically between different systems. So far, scientists have identified many bacterial defence systems, but only a few of them have been examined in detail. Recent research also suggests that there are many more defence systems out there.

Phage infecting bacterium

Nils is aiming to identify and characterise such new systems by working with a collection of bacterial strains from the Pectobacterium genus that includes pathogens responsible for significant agricultural losses due to their ability to infect a variety of crops. Nils supervised Sarah de Roode, a visiting Masters student from the Netherlands, who already made great contributions to this work.

“We are infecting the bacterial strains with various phages to identify resistance patterns that might point to the presence of immunity. This can then potentially be traced back to a defence system. If we find any previously unknown systems, we would like to gain a detailed understanding of how it works to stop the phage from replicating or infecting,” says Nils.

From a fundamental perspective, researchers know that bacteria have a massive impact on global processes such as nutrient cycles and therefore all ecosystems. Hence, everything that affects bacterial fitness and survival is of immense importance – especially for phages, given that they outnumber bacteria by about ten-fold.

Phages are being trialled as a means of pest control in agriculture. Many important crop plants such as potatoes, apples and kiwifruit are vulnerable to infection by pathogenic bacteria, and using phages to eradicate these pests is one possible solution.

Nils says “In a country like Aotearoa New Zealand which relies heavily on agriculture, this use of phages is particularly interesting. If we know how bacteria defend themselves against phages and what the phage response to this defence is, we are better prepared to develop treatments for human or plant diseases.”

Annual Report 2022

Tuesday, November 14th, 2023

Adobe Acrobat PDF file, 8.34 MB

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Te Pū Whetū o te Taiao

Aspiring to the highest pinnacle of science

This Annual Report marks our second chapter.  In it we share the adventures, wins, and big ideas that shaped 2022.

In case you missed the beginning, 2021 marked the birth of Bioprotection Aotearoa, a national Centre of Research Excellence (CoRE). Our purpose was clear—to train future bioprotection leaders and dive into groundbreaking, multidisciplinary research to tackle environmental challenges in Aotearoa New Zealand and the Pacific.

This report isn’t just some paperwork—it’s our heart and soul. It’s crafted for those at the grassroots, the stewards of the land, the food producers, the conservation warriors, and the change-makers. It echoes our principles, illustrating our commitment to empowering communities to safeguard their land and manage environmental change.

We’re excited to have you alongside as we advance as a national CoRE, supporting a resilient environment and food security.

Thank you for being an integral part of our journey in safeguarding the productive and natural landscapes of Aotearoa.


Professor Amanda Black

Director of Bioprotection Aotearoa

(Tūhoe, Whakatōhea, Te Whānau ā Apanui)


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Research Outputs 2022

Thursday, October 5th, 2023

Adobe Acrobat PDF file, 106 KB

A full list of research outputs in 2022

Download here >

Te Maramataka o Te Whānau ā Apanui

Saturday, July 1st, 2023

Featured from left to right: Matetu Herewini Jnr, Nicola Sullivan, Hanareia Ehau-Taumaunu, Rangitahi Wharepapa, Matetu Herewini, Amanda Black and Meikura Arahanga

It is Tangaroa Whāriki Kiokio, the ninth day after the full moon, and Bioprotection Aotearoa feels privileged to attend a wānanga at the headquarters of the Raukūmara Pae Maunga Project in Te-Kahanui-a-Tikirākau, also known as Te Kaha. Matetu Herewini, local Rūnanga chair, extended the invitation to this event.

During the wānanga, the Bioprotection team listened to Matetu Herewini Jnr, the son of Matetu Herewini, as he shared his knowledge about the Maramataka of Te Whānau ā Apanui.

Through waiata (songs), information sharing, and engaging activities, Matetu Herewini Jnr introduced the Māori lunar calendar and its significance to the Iwi.

The Raukūmara Pae Maunga Project, is an iwi-led conservation group that has received $34 million to heal and restore the mauri (life force) of the Raukūmara Ranges. These ranges lie in between Ngati Porou and Te Whānau ā Apanui. When the funding was announced, the two iwi and Te Papa Atawhai (DOC) collaborated to design and execute a restoration plan over the next three years.

The aim of the wānanga was to provide insights and mātauranga (knowledge) that could assist the local group in their restoration project.

By integrating this traditional knowledge with modern restoration techniques, the local group hopes to enhance their efforts and ensure that the restoration project aligns with the cultural values, environmental sustainability, and long-term goals of the Iwi.

Amanda Black, the Director of Bioprotection Aotearoa, says, “It was an absolute privilege to learn about this mātauranga, and be introduced to an extraordinary kaupapa with an Iwi-led vision. The Raukūmara Ranges feed into Te Uruwera and Whirinaki forests, which are all connected to form the largest continuous primary growth forest in the North Island. This taonga deserves a restoration response that is designed to transcend generations.”

Aligned PhD student Nicola Sullivan (Plant & Food Research) is doing fieldwork in Te Kaha, researching spiders.  While listening, Nicola made the connection to how the moon phases could have an impact on her own research.

“We learned about moon phases during which insects and spiders, among other things, hide away and aren’t as visible. When I am out hunting for spiders, I am likely to find fewer spiders during that moon phase,” says Nicola. “I think it will be helpful to record the moon phase during which I do my collections, in a similar way to the way I already note down the weather which has an effect. This could help explain any patterns I see.”

Amanda shares, “As part of our whakawhanaungatanga, the experience sparked a refreshed  sense of purpose. I can see an alignment of our vision and values between the Raukūmara Pae Maunga Project and Bioprotection Aotearoa and the work we each do.  We are grateful for the opportunity to be welcomed into their space and enrich our understanding of the rohe.”

To learn more about the Raukūmara Pae Maunga Project, visit their website >

Mānuka and Kānuka Shrublands

Saturday, July 1st, 2023

Postdoctoral Fellow Laureline Rossignaud

Laureline Rossingnaud (Pou 3.2) has published her first manuscript as a postdoctoral fellow, which is now available in Diversity and Distributions, a journal of conservation and biogeography.

Her scientific paper titled Native vegetation structure, landscape features, and climate shape non-native plant richness and cover in New Zealand native shrublands shares exciting insights into the impact of vegetation structure, landscape features and climate on non-native plant invasions across Aotearoa New Zealand in mānuka and kānuka shrublands.

Drawing from the National vegetation survey dataset surveyed between 2009 and 2014, Laureline analysed 247 permanent 20×20 meter plots distributed across Aotearoa New Zealand.  She measured the number of native and non-native plant species and their coverage at ground, understory and canopy levels.

As part of her study, she used generalised additive models (GAM) to analyse variables that had the potential to influence the richness and cover of non-native species. These variables included climate, native species richness and ground cover in relation to vegetation structure, and how landscape features surrounding these shrublands influence the arrival and establishment of non-native plant species.

This study indicates that the presence of human-made land cover in the surroundings of sample plots favour the arrival and establishment of non-native plant in mānuka and kānuka shrublands, whereas high number of native tree species and canopy cover provides resistance to plant invasions.  It highlights the value of examining both the coverage and richness of plant species at the different vegetation levels.

Although Laureline has published papers before, this is her first publication as a postdoctoral fellow.

“It’s not easy to explain that feeling when you publish a paper…excited, accomplished, and a boost of motivation to do more.” – says Laureline

Read her paper here >

Horomaka/Banks Peninsula Community Hui 2023

Friday, June 30th, 2023

Horomaka community members gather to explore resilient landscapes through informations sharing.

Meaningful engagement and multidisciplinary collaboration took centre stage at a recent gathering that brought together Bioprotection Aotearoa researchers, farmers, conservationists, and mana whenua from Horomaka.

Hosted by Bioprotection Aotearoa in Canterbury, the event aimed to cultivate stronger connections among researchers, the community, and their environment. Its overarching goal was to advance the cause of healthy and resilient ecosystems for the benefit of future generations.

Amanda Black, Director of Bioprotection Aotearoa, began the event by outlining the vision, values, and Kaupapa of the national Centre of Research Excellence. She expressed gratitude to the Horomaka community for the valuable opportunity to exchange knowledge and insights.

“The value of introducing ourselves, connecting researchers and the community, and fostering relationships cannot be underestimated” –  Amanda Black

The community heard from early career researchers who are working on understanding what makes soils resilient, future weed invasions, drivers of plant health, restorative farming practices, and adaptation pathways.

Each topic discussion reiterated the immense potential that lies in collaborative efforts spanning various disciplines and knowledge systems.

“Reaching across disciplines together, we can achieve greater outcomes that strengthen people and their environment,” Amanda emphasised.

The gathering provided a forum for participants to actively engage in dialogue, exchange ideas, and explore innovative approaches to bioprotection.

Driven by their commitment to the wellbeing of the land and future generations, community members actively participated, raising thought-provoking questions, and offering insights.

Deputy Director Phil Hulme reflected on the alignment of Bioprotection Aotearoa’s scientific efforts with the concerns of landowners and other stakeholders about emerging weed issues.

“At Bioprotection Aotearoa we have already begun to consider these emerging weed issues and the potential impact on their distributions of climate change and thus it is good to know that our science is aligned with end-user concerns.” Phil reflected.

“The landowners that I spoke to were particularly impressed by the breadth of the work being carried out on Horomaka and the enthusiasm of our early career researchers.”

Reflecting on the conclusion of the meeting, Amanda remarked, “Building deeper relationships of a collaborative nature, embracing māturaka Māori and scientific knowledge, is crucial in achieving sustainable solutions for our productive landscapes.”

She expressed a shared sense of purpose among researchers and the community, with a commitment towards continued engagement.

Insight into the effectomes of Phytophthora cinnamomi isolates

Thursday, June 22nd, 2023

Masters Student Alexandra Cox, examining her samples

Alexandra Cox’s ultimate goal is to contribute to finding solutions that will protect native plants and agricultural crops from a devastating pathogen called Phytophthora cinnamomi. Her recently completed Masters of Science with distinction at the University of Canterbury is her first step to understanding how that might be done.

P. cinnamomi belongs to a group called the water moulds, or oomycetes, which Alex describes as “a weird one on the tree of life”. Although not well understood, oomycetes are similar to fungi in many ways, but they are most closely related to algae.

P. cinnamomi is closely related to the pathogens that caused the Irish potato famine and kauri dieback disease. However, unlike these host-specific pathogens, this oomycete causes root rot or dieback in more than 2,000 plant species.

The pathogen is a huge agricultural problem in Australia, as well as 70 other countries around the world. It is becoming an increasingly serious pest in Aotearoa New Zealand, especially as the climate warms  and increases the amount of suitable environments or habitats.  Native plants of Aotearoa New Zealand are particularly vulnerable, as are agricultural crops like avocados, and forestry species. Once it has infected an area, it is very hard to eradicate.

In an effort to control P. cinnamomi, scientists are trying to understand at the genetic level how the pathogen infects its hosts, so that they can develop ways to disrupt the infection pathways. P. cinnamomi is a parasitic endophyte, which starts in the root cells and spreads through the entire plant.

Alex is searching for insights one tube at a time

To gain access to the cells, the pathogen releases proteins called effectors, which help stop the host from detecting the pathogen and make it safe for the pathogen to enter. The host plant, in turn, evolves defences against the effectors, forcing the parasite to adapt in response. This ‘evolutionary arms race’ means the pathogen and host are constantly co-evolving in a fight for survival.

An important question with P. cinnamomi is how it can keep this arms race going, when it infects such a wide range of hosts. Alex is hoping that by comparing the pathogen’s genetics in different hosts, and specifically identifying its effectors, she will gain clues to help solve this puzzle.

This is a complex challenge, however, because there are hundreds of different effectors, many of which are redundant or expendable. Also, P. cinnamomi may use different effectors on different host species, which makes it extremely adaptable.

Luckily, recent advances in genetic technology have made it easier to sequence large quantities of genomic data. Alex obtained organisms from SCION, and then extracted her P. cinnamomi DNA.   She did all of her own gene sequencing on a tiny machine about the size of a matchbox. In less than a year, she was able to sequence 10 new genomes from P. cinnamomi living on the roots of pine, kauri and fir to see how they compare. The sequences will be published online and will be a really useful tool for other researchers investigating this pathogen.

Alex plans to continue this research in her PhD, improving her sequencing even further and eventually creating a phylogenetic tree of P. cinnamomi genomes. Ultimately, she hopes to classify the pathogen’s effectors and explain what each one does.

She says, “I am so grateful for Bioprotection Aotearoa’s funding” and that she is now “more connected to other scientists than she’s ever felt.” She also enjoyed getting to learn more about science communication, cultural awareness, and “how science works in real life”.

“I have a cohort that’s been really valuable, and I’ve enjoyed learning about what’s going on at other universities and in other areas of science, from people of all ages and from all over the world. I really value these relationships and will keep them going in my PhD.”

Queenstown Research Week 2023

Tuesday, June 13th, 2023

This two day event will delve into the multidisciplinary approaches aimed at fortifying the resilience and resistance of our productive ecosystems in the face of diverse biological threats driven by climate change.

Sessions will explore themes of conservation, invasion genomics – impacts and control, persisting pathogens, and the social science behind valuing our landscapes.

Leading experts will join us to discuss the concept and application of Indigenous methodologies, intellectual property, and data sovereignty in research.

Whether you are early in your career, or a seasoned researcher, there will be a session to explore what a career in bioprotection looks like in this current research climate.

In collaboration with Genomics Aotearoa, and their Indigenous Genomics Platform, we are proud to showcase the power of holistic approaches that span ecological, molecular, Indigenous knowledge and socioeconomic sciences, within a cultural values framework.

This event will highlight how these comprehensive strategies can offer fundamental solutions for the sustainability of the primary sector, which is integral to providing economic, social, and environmental wellbeing for Aotearoa New Zealand.


Programme | Day 1 | Thursday 31st August

Session 1:

Hungry for advice: breakfast, posters and career advice for a career in bioprotection

Organised by Dr Steve Wakelin, SCION

Session 2

Concept and application of indigenous methodologies, intellectual property and data sovereignty in research

Organised by Prof Amanda Black (Tuhoe, Whakatōhea, Te Whānau ā Apanui), Lincoln University

A panel discussion featuring

  1. Linda Tuhiwai Smith, (Ngāti Awa, Ngāti Porou, Tuhourangi)
  2. Stacey Whitiora (Ngāti Mahuta ki te Hauāuru, Waikato)
  3. Lynell Tuffery Huria (Ngāti Ruanui, Ngāruahine)
  4. Melanie Mark Shadbolt, (Ngāti Kahungunu ki Wairarapa, Ngāti Porou, Te Arawa, Ngāti Raukawa, Ngāti Tuwharetoa, Te Ātiawa)

Click here for information about speakers

Session 3:

Partnering with communities to conserve our taonga species

Organised by Dr Nathan Kenny, University of Otago

Session 4

Invasion genomics, impact and control

Organised by Prof Ian Dickie, University of Canterbury

Programme | Day 2 | Friday 1st September

Session 1

Valuing our landscapes

Organised by Ann Brower, University of Canterbury

Session 2

Microbiomes in landscape

Organised by Dr Hanareia Ehau-Taumaunu (Ngāti Uepōhatu, Ngāti Porou, Te Ātiawa, Te Whānau-a-Āpanui, Ngāpuhi), Plant & Food Research

Session 3

Preventing the persistence of pathogens and pests

Organised by Prof Matt Templeton, Plant & Food Research

Session 4

Tackling i4: integration, interdisciplinarity, implementation & impact

Organised by Dr Franca Buelow, University of Canterbury


Fionnuala Bulman spills the soil on her project

Monday, March 27th, 2023

PHD Student Fionnuala Bulman, sampling soil with a soil corer

PhD Student Fionnuala Bulman (known as Finn to her peers) has a background in medical microbiology, but her passion for the outdoors and interest in the natural world motivated her to make the leap from biomedical to environmental research.

Taking up a PhD with Bioprotection Aotearoa, Finn is investigating how land-use shapes Arbuscular mycorrhizal fungi communities and how these communities are linked to the resilience of natural and managed ecosystems in New Zealand.

Arbuscular mycorrhizal fungi (AMF) are microbes that colonise the roots of terrestrial plants, forming structures that look like ‘little trees’ inside root cells, and extend microscopic fungal threads called mycelium out into the soil.

They form a mutually beneficial relationship, providing plants with nutrients from the soil, and receiving carbon generated by the plants through photosynthesis.  Soil structure is also improved by the network formed by fungal mycelium, resulting in increased water-holding capacity and gas exchange.

Research in this fungal network has become a hot topic in recent years, with scientists working to advance understanding of the diversity of AMF species, their function in plant-soil ecosystems, and the hidden underground networks they form.

Finn’s field work is located in Te Kaha, the Bay of Plenty. It’s a relatively small area with a variety of land uses present.  With maize fields and kiwifruit orchards patch worked across the landscape and bordered by native bush, it’s an ideal site to conduct this research

By collecting soil samples from these three distinct ecosystems, and comparing the diversity of AMF species found in each, Finn is hoping to identify how land-use shapes AMF communities.

“Studies have shown that mycorrhizal fungal communities can change significantly across space and time. Samples taken even a meter apart can contain very different fungal species and the same site sampled in winter and summer may also show very different communities” says Finn.

Agricultural systems, management practices, weather events, and seasonal changes can all potentially influence what happens below ground. As such Finn is using a structured sampling system across the Te Kaha landscape, to capture some of this spatial variation for each ecosystem (18 in total).  She is also sampling quarterly to incorporate some seasonal variation into the sampling.

With this method, Finn hopes to build a more comprehensive picture of the AMF species present in Te Kaha ecosystems and any changes within the AMF communities between seasons.

This first phase of Finn’s research project will then determine whether AMF communities are affected by human input such as agricultural management practices or if natural changes in conditions such as seasonal weather patterns actually drive these shifts.

“Are the AMF communities stable or are there big shifts that line up with human management, such as annual planting and harvesting of maize? How does this compare to the effect of pesticide application in kiwifruit orchards or the relatively undisturbed native forest?” Finn queries

Māhoe seedlings, a native plant found throughout the forest in Aotearoa New Zealand

The second phase is to inoculate plants with the AMF communities collected in Te Kaha and expose these plants to conditions that model future climate- change scenarios, involving higher temperatures and higher CO2 levels. Host plants include the Bruno-Hayward variety of kiwifruit, a silage maize cultivar currently grown in Te Kaha and māhoe, a native plant that is found throughout the forest in Aotearoa New Zealand.

Finn hypothesises that AMF are important for plant resilience and therefore plants inoculated with AMF will cope better with these conditions. She hopes that this information can support agribusiness in Te Kaha to make informed decisions about the future of their whenua, for example future land use and management to promote resilient soil and plants.

The data that Finn collects from her sampling in Te Kaha will also contribute to a global project aiming to map mycorrhizal fungal networks world-wide. SPUN (Society for the Protection of Underground Networks) is a recently founded research organisation, on a mission to advocate for the protection of mycorrhizal networks. “I really support that kaupapa” says Finn “as once we know what’s there and can prove it is important on an ecosystem scale it becomes much easier to push for policies to protect what we have”.

After reading about the project in a news article, Finn wondered what sort of methods they would be using for sampling and was encouraged to reach out to Dr. Toby Kiers, the Executive Director & Chief Scientist of SPUN.

“She’s very well-known in mycorrhizal research” Finn shares “and so I was surprised to quickly receive a reply and guidance from Toby herself. It was lovely to realise that there was this network of support and opportunity for collaboration with scientists who were willing to invest time into answering the questions of an early career researcher like myself”.

As a result of these conversations, Finn is using methods similar to those developed by Toby and her team and therefore the data she produces will be comparable with that of other contributors around the world.

“Hopefully, the data that I provide will be a useful contribution to the global database on mycorrhizal diversity. Alongside my own PhD work, I’m really excited to see how that project and whole movement of mycorrhizal research progresses in the next few years – it’s an exciting time.”



Summer Scholar Presentations 2022-2023

Thursday, March 23rd, 2023

PLAY VIDEO | Summer Scholars answer quick fire questions

Bioprotection Aotearoa (BA) is proud to foster an inclusive learning environment that awhi (care and nurture) our early career researchers through broad networking opportunities. Over the summer of 2022-2023, we welcomed a total of 10 students into our summer scholarship programme.  They were introduced to research through experiences in the lab and out in the field, and mentored by our BA whānau to develop their practical skills.

Our Summer Scholars presented their work in an online event to a large audience from around Aotearoa.  Professor Margaret Stanley (The University of Auckland) hosted this event and says “the students all gave fascinating research talks and were clearly excited about doing science”

PLAY VIDEO | Watch the full presentations

Margaret reflects how on how COVID reduced opportunities for this cohort to get practical skills and says “all of them had learnt a variety of new skills and were pleased to be able to spend lots of time in the field and lab. Thanks to all the supervisors, ECRs and lab groups that supported our summer students – it makes a huge difference when they feel that manaakitanga!”