Author Archive

Get to know Jade Gibson

Wednesday, September 15th, 2021

Where I’m from

Of Ngāti Porou descent, I grew up in the Bay of Plenty, spending most of my childhood in Tauranga and Whakatane. I love the beautiful beaches, the waterfalls and most of all visiting my marae on the East Coast – Whareponga.

How I became part of Bioprotection Aotearoa

I majored in environmental science and geography for my Bachelor of Science. I always knew I wanted to study something to do with the environment because of my deep appreciation for Papatūānuku and my call to help her. As I finished my degree, I realised that I had not exactly fulfilled that purpose.

In 2020, I decided to complete my Honours, investigating how much power is shared in the co-governance of kauri dieback up north. I started to uncover the downfalls of some of these programmes. There was a complete lack of partnership and collaboration, while Mātauranga Māori was largely excluded or unsupported. This provoked me to continue on to a PhD.

My research subject

For my PhD I am researching how braiding Mātauranga Māori and western science can help to inform biosecurity threats in New Zealand – with a focus on kauri, myrtle rust, and pest fish. I hope to connect to different iwi and hapū and support them in sharing their cultural narrative of these issues and show the strength in using Mātauranga Māori in solving them.

I also hope to show the importance of engaging and partnering with Māori in all areas of environmental protection. I strongly believe that true collaboration is the only way we can save our environment.

What I like most about my research

The most amazing thing about my research is the opportunity to reconnect to my Māori heritage. As a young scientist growing up in a very western world, I had lost touch with who I truly am. Through reconnecting to Māori culture, I have felt a strong reconnection to myself. I hope that I can learn te reo and delve deeper into my whakapapa, that I can continue to support and advocate for the amazing values, knowledge, and principles, that the culture holds.

What I’d like to do once I’ve finished my study

I would like to continue to use Mātauranga Māori to help inform environmental decisions. I’d like to work with councils, iwi, government, community, to engage with Māori and incorporate Māori values and cultural narratives into our decisions.

What I like to do outside of study

I love to explore nature. Whether it is skiing, hiking, surfing, or foraging for wildflowers and food, I love being active and outdoors. I will never say no to an adventure! When at home, my happy place is either in the kitchen cooking for friends or in the backyard gardening and practicing yoga.

My social media accounts

You can find me on LinkedIn and Instagram.

Get to know Nils Birkholz

Wednesday, September 15th, 2021

Where I’m from

I’m from near Hannover in Germany – a region urban enough that Otago induced a bit of a culture shock when I first arrived here.

How I became part of Bioprotection Aotearoa

I was introduced to the New Zealand science scene when I came here for an internship during my MSc, and then I started my PhD in Peter Fineran’s lab on bacterial defence systems. After my PhD, I was given the exciting opportunity to keep working in this field as part of Bioprotection Aotearoa.

My research subject and how I became interested in it

During my PhD, I investigated bacterial defence systems such as restriction–modification and CRISPR–Cas, as well as anti-CRISPR proteins, a counter-defence mechanism evolved by bacteriophages – the viruses that infect bacteria.

I became interested in CRISPR–Cas during my studies at the Technische Universität Braunschweig in Germany when I read a review paper by last year’s Nobel laureate Emmanuelle Charpentier on small RNAs and their role in CRISPR defence. Coincidentally, Charpentier had a lab in Braunschweig at that time and I got in touch to see if I could start working with her as a way into the CRISPR field. Luckily, this never came to fruition and I instead travelled to Dunedin to join Peter’s lab – which I believe was the much better choice.

In this role, I am hoping to identify and characterise so-far unknown defence mechanisms, which might lead to interesting new applications – after all, the discovery of the popular gene editing tool Cas9 resulted from basic research like this.

What I like most about my research

Aside from generating new knowledge – I guess that’s why all of us do research – I also really like trying to find creative ways to communicate these findings in writing and through images. Believe it or not but I did enjoy some aspects of working on my thesis!

The impact I hope my research will have

There is still a lot we can learn when it comes to the interactions between bacteria and phages, and defence and counter-defence systems are one crucial aspect of this. I hope my research can help to broaden our understanding of this interplay. Phages can be used as agents against human or plant pathogens, and many bacterial or phage proteins have proven very useful in generating versatile tools. I hope to continue this tradition and help provide more examples of basic research as a source of great innovations.

What I like to do outside of work

I like to go running on the streets and trails in and around Dunedin, do amateur photography, check my plants way too often for whether they might have become a millimetre taller, look up places that could be nice for tramping … and sometimes actually go there!

Contact me about

Anything! Whether you want to know more about the research we’re doing, have ideas of potential overlaps or collaborations, or whatever else you might be interested in. I’m also very keen to work on my science writing and communication skills, so I’d be happy to hear from you if there are any opportunities available.

My social media accounts

I’m on Twitter as @NilsBirkholz

Get to know Michelle Boyle

Wednesday, September 15th, 2021

Where I’m from

I grew up on the West Coast, but came to Christchurch during my high school years.

How I became part of Bioprotection Aotearoa

It’s a long complex story, intertwined with my life as a postgrad student, best answered in the next question!

My research subject

Although it’s not applicable to my work for Bioprotection Aotearoa, I am a marine turtle biologist. When I was studying for my MSc in the midst of a Dunedin winter a scholarship was advertised to undertake a research project at the University of the South Pacific, Fiji – so of course I signed up! While in Fiji I studied the population demographics of marine turtles that were being harvested and sold in the markets. I later won a PhD scholarship at James Cook University in Townsville, Queensland, where I continued studying marine turtles – this time investigating the ‘lost years’, the cryptic post-hatchling life stage.

After my PhD I worked on Boigu, a remote island in the Torres Strait for the local council and later for the Queensland Government. This job had me racing around on small ‘catch’ boats, from which we would ‘rodeo’ turtles and dugongs. Turtle rodeos are a real thing!

After that I juggled private consultancy, establishing and managing a bike shop, and becoming a mum. Eventually, that brought me back to New Zealand, where I applied for a job at Lincoln University, and got it!

What I enjoy most about my job

As the contracts manager of Bioprotection Aotearoa I work with a wide range of people every day. I am lucky to share an office with great people, and to be able to share in the journey of our students, to communicate with our researchers from all around the country and see the successes of the science programmes.

What I like to do outside of work

I live at the base of the Port Hills, so I love to explore the tracks when I can. I especially love the occasional Rogaine to get off the regular beaten tracks.

Contact me about

Contracts, project budgets, reporting, and travel.

Get to know Fionnuala Bulman

Wednesday, September 15th, 2021

Where I’m from

I was born in Bristol, England but emigrated with my family to New Zealand at the age of 12, settling in the Motueka Valley. I’ve since called South Island places home, including Dunedin, Queenstown and currently Arthur’s Pass, and have spent time in Canada and Germany.

How I became part of Bioprotection Aotearoa

I completed a Bachelor of Biomedical Sciences at the University of Otago, then after a few years away from study, a Master’s degree in molecular medicine at the Friedrich-Schiller University in Jena, Germany.

Halfway through the Master’s I realised I couldn’t imagine life in a pathology lab and environmental sciences would more closely align my passion for the outdoors with my career. I had always been most interested in microbiology, so soil microbial ecology seemed a perfect field to segue into. I’ve spent the last few years trying to make that a reality, including taking a course in environmental management at the Southern Institute of Technology and spending a summer getting my hands dirty as a conservation worker removing wilding pines from the Mackenzie Basin. When Eirian Jones suggested I might be interested in this PhD scholarship it seemed too good an opportunity to let pass by.

My research subject

My research topic is the role of plants in creating resilient soils that can withstand stresses such as drought and disease, particularly when exacerbated by climate change.

I would love to focus on the role of mycorrhizal fungal networks in creating more disturbance-tolerant ecosystems, from the perspective of soils, vegetation, and human communities.

I find mycorrhizal fungal networks fascinating because of their complexity and the fact they are still so difficult to study in the field. Research has looked at their influence in forest ecosystems, but there is still a lot to learn about their function in agricultural systems. It would be great if advancements in knowledge of these networks could help us to manage ecosystems more efficiently and sustainably.

What I like most about my research

Although I haven’t started my research yet, I am enjoying diving into the literature of soil microbial ecology. As this is a very different area to my previous studies there is a lot to learn. Having freedom to develop my research questions within the broad initial topic and considering what kind of experiments I will need to carry out feels exciting.

What I’d like to do once I’ve finished my study

I would love to find a job that combines field work with office or lab work, as being outside and connecting with the ecosystems I am studying is important to me. I’d like to be able to travel as part of my work and would love the chance to visit Antarctica as a researcher and live at Scott Base for a season.

What I like to do outside of study

Get outside! In the summer this is mainly in the form or tramping and in the winter skiing and mountaineering. We are so fortunate in New Zealand to have such an incredible network of trails and huts – there is always more to explore!

My social media accounts

You can find me on Instagram

From the Directors, Spring 2021

Wednesday, September 15th, 2021

Tēnā koutou,

Welcome to the first internal newsletter of Bioprotection Aotearoa, our new Centre of Research Excellence. It is an exciting time, albeit now overshadowed by a resurgence in COVID. We hope you are all staying well and safe, whether you are in Auckland and still in lockdown, or with the lesser restrictions in the rest of the country.

We hope this disruption has not caused too many issues. If there is anything that BA can do to help, please contact any of the management team.

As the CoRE gets underway there are a lot things going on, including signing partnership agreements, advertising for students and postdocs and planning research. Most partner organisations have signed the Collaborating Parties Agreement, and once they all have we can sign the research agreements, for each university or CRI.

You may have seen the adverts for PhDs and postdocs that have been published on our website, and promoted through social media. It would be great if you could distribute and promote these through your own networks.

We have held a first meeting of the new advisory board, under our Co-Chairs Matua Henare Edwards and John Rodwell, which was a very good getting-to-know-each-other session and also a look at a new risk register. We held a first meeting of the Collaborating Partners representative group, which has members from each organisation. These groups will help us coordinate not just the science, but all efforts across organisations. We are also looking at our needs for support and will be advertising outreach and other positions soon.

The other area of a lot of activity is of course research planning. The teams were to be out scouting new locations for field work and meeting with iwi and other groups that can partner, but unfortunately lockdown has paused that. That will commence as soon as practical. As a result, we don’t have any research updates in this issue of enCORE, but we’ve taken the opportunity to publish several staff and student profiles, to help us get to know each other.

Noho ora mai, stay well and look after yourselves.

Amanda and Travis

What’s in a brand?

Monday, July 19th, 2021

Creating the new brand and logo for Bioprotection Aotearoa was a collaborative effort, involving many different people with many different roles in the new Centre of Research Excellence.

It started with a one-day branding workshop involving researchers, directors, kāhui, and admin team members, from which we created a kaupapa positioning strategy. We then briefed a designer.

Designer Kim Hickford produced three alternatives, each emphasising a different aspect of Bioprotection Aotearoa’s kaupapa.

The logo we chose, with significant input from our Co-Chair Henare Edwards and the kāhui, is based on the three pou, or pillars of key research for Bioprotection Aotearoa. Each pou is a stylised koru shape to represent growth and strength. The three pou stand proudly, almost like people or sentinels, each one gaining strength from its neighbour, quietly guarding the environment.

The curve stretching across the bottom represents the foundation of the whare, Papatūānuku, mother Earth.

Our logo encapsulates the essence of Bioprotection Aotearoa – working collaboratively to tackle the bioprotection challenges we face and protect our environment.

What is Bioprotection Aotearoa?

Monday, July 19th, 2021

Bioprotection Aotearoa is a new Centre of Research Excellence, built on the whakapapa of the Bio-Protection Research Centre. However, it is not a simple continuation – it is an evolution.

Bioprotection Aotearoa adopts a new approach to bioprotection research in Aotearoa New Zealand. Excellent science is still at its core, but the way of doing that science is more inclusive and holistic. It is guided by a Māori values framework – Taiao – to protect our productive landscapes from pathogens, pests, and weeds.

Our research is structured around three pou, or pillars, which support the whare of our research.

Pou titirangi – piercer of the heavens

The first pou guides our research to DEFINE a healthy, productive ecosystem. It is led by Prof Jason Tylianakis (University of Canterbury) and Dr Julie Deslippe (Victoria University of Wellington).

The three projects in this pou cover integrated measurement of healthy ecosystems, processes that promote productive ecosystems, and a new framework to assess ecosystem health in Aotearoa New Zealand.

Pou tokomanawa – the heartbeat of the whare

The second pou guides our research to DEFEND against pathogens, pests, weeds, under a changing climate. It is led by Dr Monica Gerth (Victoria University of Wellington) and Prof Matt Templeton (Plant & Food Research, University of Auckland).

There are four projects in this pou, covering the mechanisms of microbiota-mediated protection against plant pathogens, genetic and genomic approaches to controlling plant pathogens and insect pests, and exploring the molecular basis of pathogen host specificity.

Pou nuku-a-rangi – shifting throughout the heavens

The third pou guides our research to DESIGN ecosystems that are more resilient and resistant. It is led by Dr Steve Wakelin (Scion) and Assoc Prof Amanda Black (Lincoln University).

The three projects in this pou cover creating healthy, disease-resistant and climate-resilient soils, designing future forestry, and creating effective socioeconomic and governance models that lead to resilient ecosystems.

Another research theme extends across all pou and supports them: recloaking Papatūānuku. This is an indigenous socio-ecological restoration model using mānuka and kānuka to promote native biodiversity and restore our whenua.

It aims to define the links between humanity and the natural world, resolve the value of mauri across ecosystems, and show how ecosystem restoration underpins community wellbeing. It is led by Prof Nick Roskruge (Massey University) and Dr Nick Waipara (Plant & Food Research, University of Auckland).

“Bioprotection Aotearoa is doing exactly what a Centre of Research Excellence should do,” says Co-Director Travis Glare. “We are bringing together a national team of experts, to push the boundaries of science and train the next generation of leaders in the field.”

Fellow Co-Director Amanda Black says she is very excited to be leading a CoRE of talented people to carry out the kind of research that Aotearoa New Zealand needs. “I’m hoping we will grow together as a team to achieve our desired outcomes and impacts – the main one being healthy productive landscapes guided by Te Ao Māori values.”

Closing in on answers to kauri dieback

Wednesday, July 14th, 2021

How have land-use changes affected the growth and survival of Phytophthora agathidicida, the invasive oomycete that causes kauri dieback?

Kauri (Agathis australis), one of New Zealand’s most iconic native trees, is culturally significant to Māori and functions as an ecological foundation species. However, after logging and clearance for agriculture only around 1% of the original kauri forest remains. These remnant, fragmented kauri forests are now threatened by the spread of kauri dieback.

Based in Waipoua and in partnership with Te Roroa Iwi, we set out to understand what part these land-use changes have played.

We found that surrounding land uses of exotic pine (Pinus radiata) and pasture (common pasture species) led to higher growth and sporulation rates of P. agathidicida than in than kauri forests soils, creating potential disease reservoirs. Pine also significantly altered soil microbial community composition, including the loss of microbial taxa linked to plant health. This highlights that historical disturbance of the soil environment surrounding kauri forests may increase their susceptibility to invading plant pathogens.

We also investigated how kauri dieback may cause secondary, cascading impacts that affect long-term forest ecosystem functioning. We looked at the differences between symptomatic and asymptomatic mature kauri in terms of diversity, taxonomic composition and functional genes related to carbon and nitrogen cycling of soil microbial communities.

We found significant differences in the fungal diversity and the fungal and bacterial community composition between asymptomatic and symptomatic kauri. Several microbial taxa known for supressing plant disease, such as Penicillium, Trichoderma, Enterobacteriacae and Pseudomonas, were significantly more abundant in asymptomatic kauri soils.

These results provided a promising direction for the discovery of micro-organisms that suppress kauri dieback. As well, significant differences in the composition and abundance of microbial genes related to carbon and nitrogen cycling highlight the potential long-term impacts of dieback disease on the health and functioning of kauri forests.

Relationships matter to invading species

Wednesday, July 14th, 2021

Prof Jason Tylianakis collecting field data

What role, if any, do the interactions between species play in determining the success of invasive exotic plants on New Zealand ecosystems?

Using a combination of field observations, field-based experiments, large-scale experiments, and advanced molecular and statistical tools, the Bio-Protection Research Centre project “Achieving Bioprotection in New Zealand ecosystems” (Project 3) investigated this question. And the answer was surprising.

Our research largely reversed the long-held paradigm of “enemy escape”, the theory that a loss of species interactions contributes to the success of exotic species. Instead, we showed that species interactions mediate ecosystem processes and functioning in complex and surprising ways.

In field-based experiments, we showed that exotic plants have stronger, rather than weaker, interactions with herbivores and with beneficial and pathogenic fungi, and so facilitate further invasions. We also showed parallel patterns in productive ecosystems, where land-use change is associated with an increased, rather than decreased, diversity of plant pathogens, driven by changes in the composition of plant species.

Our research moved beyond descriptive approaches to direct scientific tests, by creating 180 independent soil-biota-plant-herbivore communities in controlled conditions. This experiment provided one of the first direct tests of community-level interactions involving exotic and native plants with soils, fungi, and herbivores.

We conclusively showed that the impacts of exotic plants on multiple ecosystem functions are mediated by biological interactions with soil biota and invertebrate herbivores. Exotic plants in these ecosystems show much higher growth rates than natives, and are able to dominate communities despite supporting high populations of herbivores and pathogens. Again, these interactions may be key to success, with pathogen spillover on to natives contributing to exotic plant dominance.

Our research showed that the global movement of species results in stronger and more variable interactions, rather than interaction loss. These strong species interactions are crucial to plant invasion success and impacts in both native ecosystems and exotic-dominated landscapes, such as agriculture and forestry.

Progress against pathogens

Wednesday, July 14th, 2021

Dr Richard Winkworth, with one of the field-based assays in development.

Plant pathogens pose an ongoing risk to agriculture and the conservation estate in New Zealand. In the past decade the country has experienced devastating epidemics caused by Pseudomonas syringae pv. actinidiae (Psa) on kiwifruit and Phytophthora agathidicida on kauri.

In responding to these epidemics, research teams from Project 3 made significant contributions to:

  • Pathogen detection, including a field-based LAMP assay for P. agathidicida, and PCR-based assays for Psa. LAMP-based assays are a significant advance over plate-based baiting assays, as they are generally cheaper and more robust.
  • Epidemic origin, including the first paper postulating the timing of the origin of P. agathidicida in New Zealand, and a highly cited paper on evolution of Psa.
  • The molecular determinants of disease, making substantial progress in understanding how P. agathidicida and Psa cause disease.
  • Understanding the relationship between excision and Mobile Genetic Elements (MGEs), including Integrative and Conjugative Elements (ICEs). These are crucial entities in the evolution of prokaryotes, as they are the main source of laterally acquired genetic information. We made crucial advances in understanding the relationship between excision and transfer rate, resulting in several high-profile publications in internationally reviewed journals.

The P. agathidicida team particularly focused on engaging with Māori. We studied the expression of P. agathidicida genes in kauri tissue in partnership with Te Roroa and the Scion Healthy Trees Healthy Future programme. We developed the hybrid LAMP assay in partnership with Te Kawerau ā Maki and Te Roroa, and used it in partnership with iwi/hapu in Auckland, the Kaipara, and Northland, where it has been, or is being, used to inform decision-making.

One very important outcome of our research has been the high calibre of new researchers we have trained and supported. Drs Carl Mesarich and Jay Jayaraman now have permanent positions with Massey University and Plant & Food Research. The late Dr Pierre DuPont was employed by ESR. Several former students have also gone on to permanent research positions within New Zealand, ensuring bioprotection science is in good hands.