This research theme is focusing on the ‘disease triangle’: host susceptibility, the pathogen and the right environment for disease expression. Plants and pathogens can both be influenced by a number of factors such as disturbance, topography, weather, soil type and pest control. These factors can, in turn, affect how the plant pathogens adapt to New Zealand’s environment. Our team are investigating the role environmental factors play on disease expression and severity, as well as researching the pathogen genomes. The knowledge we gain will contribute to improving surveillance, control, management and conservation efforts, and we hope to discover new ways to mediate these diseases. We are testing an innovative kaupapa Māori programme known as Te Whakahononga in this theme. This provides the mechanism for linking scientists to mana whenua in affected kauri and myrtle ngāhere, while enabling mana whenua to lead field work in their rohe and apply mātauranga based assessments of ngahere health and relationships. __Theme Co-leads:__ - Juliane Chetham, Chetham Consulting Ltd. - Nari Williams, Plant and Food Research Ltd.
RA3 PAPER: Variability in phosphite sensitivity
###Variability in phosphite sensitivity observed within and between seven *Phytophthora* species### **January 2022** **Hunter S, McDougal R, Williams N, Scott P. 2022. [Variability in phosphite sensitivity observed within and between seven *Phytophthora* species.](https://link.springer.com/content/pdf/10.1007/s13313-021-00846-5.pdf) Australasian Plant Pathology. ** **ABSTRACT** Phosphite is used to control and manage many phytophthora diseases in horticultural systems worldwide and natural ecosystems in Australia, Africa, New Zealand and parts of Northern America and Europe. Phosphite does not kill *Phytophthora* species, but inhibits growth while also stimulating host defence responses. *Phytophthora* species differ in their underlying tolerance to phosphite and isolates have been shown to acquire tolerance after prolonged exposure. Intra- and inter-specific variability in phosphite sensitivity is of interest to determine the efficacy and sustainability of phosphite for the treatment of phytophthora diseases, which continue to spread globally. In this paper seven *Phytophthora* species were tested for their sensitivity to phosphite in vitro in a mycelial growth experiment, including *Phytophthora agathidicida*. **KEYWORDS** *Phytophthora*; Phosphite; Interspecific; Intraspecific Variability; Management
RA3 PAPER: Impacts of phosphite on Phytophthora community in soil
###Impacts of phosphite treatment on *Phytophthora* community assemblages and inoculum abundances in *Phytophthora*-infected forest soil### **December 2024** **Hunter S, Waipara N, Burns B, Scott P, Williams N. 2024. [Impacts of phosphite treatment on *Phytophthora* community assemblages and inoculum abundances in *Phytophthora*-infected forest soil](https://doi.org/10.1016/j.tfp.2024.1006870). Trees, Forests and People 18: 100687** **ABSTRACT** *Phytophthora* are causing declines in forest tree species worldwide and the chemical control treatment, phosphite, is the only treatment consistently shown to provide some protection to natural ecosystems from *Phytophthora* diseases. Phosphite inhibits *Phytophthora* growth and sporulation whilst boosting defence responses in the plant host. It is unclear, however, the extent of the impact of phosphite on *Phytophthora* species assemblages and inoculum abundances in soil around trees following treatment within natural ecosystems. In New Zealand, kauri (*Agathis australis*), an endemic and threatened foundation species, suffers from a dieback disease primarily caused by *Phytophthora agathidicida*. Phosphite is applied by trunk injection to kauri and has been shown to improve resin ‘bleed’ symptoms from basal trunk lesions and to promote recovery of thinned canopies. *Phytophthora* community and inoculum abundance were investigated in response to phosphite treatments at two field sites (Huia and Waitoki) in infected kauri stands in Auckland, New Zealand. At Huia, soil sampling and tree health surveying were conducted in November 2023 on trees treated with phosphite in 2012 as part of an earlier study. At Waitoki, the response to phosphite treatment was monitored 6 and 18 months following treatment. *Phytophthora* species were detected using soil baiting and metabarcoding of Environmental DNA (eDNA) from soil and quantified with qPCR of root and soil DNA. Three species were detected with soil baiting (*P. agathidicida, P. cinnamomi*, and *P. multivora*) and two additional species with metabarcoding (*P. pseudocryptogea,* and an unknown clade 7 species similar to *P. europaea*). *Phytophthora cinnamomi* was the most abundant species, followed by *P. agathidicida*. Both species were more likely to occur together than by chance alone and were associated with declining tree health. The *P. europaea*-like species was in approximately 50 % of the samples and was less likely to occur in roots with poorer health, or in association with *P. agathidicida*. The abundance of *P. agathidicida* inoculum was lower in the soil around the phosphite-treated trees than around the untreated control trees 1.5 years after treatment at Waitoki. Phosphite halted the lateral expansion of basal resin bleeds, and resin viscosity was reduced. Not only did phosphite treatments improve kauri dieback symptoms, but the phosphite treatments potentially had a direct impact on the epidemiology of the disease by reducing inoculum load around treated trees, with direct implications for disease management as an effective way to protect uninfected areas and minimise the spread of inoculum from infested zones. **KEYWORDS** *Phytophthora agathidicida*; Phosphite; New Zealand; *Agathis australis*; Epidemiology
RA3 PAPER: Phytophthora associated with kauri
###*Phytophthora* Communities Associated with *Agathis australis* (kauri) in Te Wao Nui o Tiriwa/Waitākere Ranges, New Zealand### **April 2024** **Hunter S, Horner I, Hosking J, Carroll E, Newland J, Arnet M, Waipara N, Burns B, Scott P, Williams N. 2024. [*Phytophthora* Communities Associated with *Agathis australis* (kauri) in Te Wao Nui o Tiriwa/Waitākere Ranges, New Zealand.](https://www.mdpi.com/1999-4907/15/5/735#) Forests 15(5) 735** **ABSTRACT** Studies of *Phytophthora* impacts in forests generally focus on individual species without recognition that *Phytophthora* occur in multispecies communities. We investigated community structure of Phytophthora species in the rhizosphere of *Agathis australis* (kauri) in Te Wao Nui o Tiriwa / Waitākere Ranges, New Zealand, in the context of kauri dieback disease expression. Soil sampling and tree health monitoring was conducted on 767 randomly selected mature kauri trees. *Phytophthora* species were detected using both soil baiting and DNA metabarcoding of eDNA. Four species were detected with soil baiting (*P. agathidicida, P. cinnamomi, P. multivora*, and *P. pseudocryptogea*) and an additional three species with metabarcoding (*P. kernoviae, P. cactorum/P. aleatoria* and an unknown clade 7 species). *Phytophthora cinnamomi* was the most abundant species and was distributed throughout the forest. Both *P. multivora* and *P. agathidicida* were limited to forest edges, suggesting more recent arrivals. *P. agathidicida* presence was strongly correlated with declining canopy health, confirming its role as the main river of kauri dieback. The limited distribution of *P. agathidicida* and infrequent detections (11.0% samples) suggests that that this species is spreading as an introduced invasive pathogen and provide hope that with strategic management uninfected areas of the forest can be protected. The frequent detections of *P. cinnamomi* and *P. multivora*, from symptomatic trees in the absence of *P. agathidicida* suggest more research is needed to understand their roles in kauri forest health. **KEYWORDS** *Phytophthora; Agathis australis*; kauri dieback; soil baiting; metabarcoding; New Zealand; epidemiology; invasive pathogen; forest management
RA3 PRESENTATION: Spatial variation in Phytophthora detection
###Spatial variation in *Phytophthora* detection within infected areas### **May 2023** **Williams NM, Hunter S, Arnet M, Donahoe C, Carroll E, Hosking J, Horner I. 2023. Spatial variation in *Phytophthora* detection within infected areas. Kaurilands Summit, Whangārei, New Zealand, 11/05/2023.** Presented by Nari Williams.
RA3 REPORT: Effect of soil pH on Phytophthora agathidicida
###Investigating the growth, reproduction and survival of *Phytophthora agathidicida* under different soil pH### **2033** **Davies B. 2023. Investigating the growth, reproduction and survival of *Phytophthora agathidicida* under different soil pH. Unpublished MSc Report, Massey University. ** **NOTE** This Master's report is not publicly available online. For further information please contact supervisor, Dr. Nari Williams at Plant and Food Research: [Nari.Williams@plantandfood.co.nz](mailto:Nari.Williams@plantandfood.co.nz) **ABSTRACT** In order to better understand the biosystem around kauri and *P. agathidicida*, this research focuses on elucidating environmental and genetic parameters that affect *P. agathidicida*, particularly in connection to the poorly studied aspect of pH. In this study, the pH levels at two *P. agathidicida*-containing kauriland sites were surveyed and a soil pH range of 3.42 – 7.02 detected, with site-specific averages of 4.36 (Ngāti Rua) and 4.96 (Waitākere Ranges). Detection of *P. agathidicida* was limited to the lower 89% of the total pH range, at 3.42 – 6.64, but this was not statistically significant. Another species *Phytophthora cinnamomi* was also surveyed, and contrastingly found to be present in the upper 88% of total pH range, at 3.84 – 7.02. This was a statistically significant result, and suggests that the two *Phytophthora* species have different pH limitations. The presence of *P. agathidicida* in these soils appeared to be driven by factors other than pH, with *P. agathidicida*-containing soils at an average pH of 5.49 for the Waitākere Ranges and an average of 4.52 for Ngāti Rua. When looking at growth parameters, rather than presence alone, *P. agathidicida* was able to grow in minimal media across the assayed range of pH 5.1 – 6.9, but displayed significantly higher optical density (OD) increases in two distinct peaks of pH 5.1 and 6.8. Looking at sporulation, no pH-dependency was seen across an assayed range of 3.5 – 8, though formation of immature sporangia, mature sporangia and oospores all had significant isolate-dependent variation. One further step in creating a deeper understanding of this biosystem lies in exploring the genetic elements of *P. agathidicida*, through pathogenicity-related genes from other genetically similar microorganisms. While pH-modulated pathogenicity genes are of particular interest, it would be remiss to limit exploration to this spectrum, hence this delimitation was not applied. From a total of 22 pathogenicity-related genes in selected from other *Phytophthora* spp., 18 potentially orthologous coding sequences were identified in the *P. agathidicida* genome, five of which showed differential expression during infection. Three of these five putative proteins had upregulation during infection, and likely correspond to an aspartyl protease (AP), an NLP effector, and a PDR-like ABC transporter. Additionally, five pathogenicity-related genes from non-*Phytophthora* microorganisms, with pH-modulated behaviour, were investigated. Four of these proteins corresponded to *P. agathidicida* coding sequences, although with high divergence. One of these sequences, which may be distantly related to the fungal pH-responsive transcription factor PacC, showed a significant increase in expression during infection. It is hoped that the findings in this report will increase the understanding of pH parameters in *P. agathidicida* growth, and provide direction for further research prospects within the host-pathogen relationship responsible for kauri dieback.
RA4 PAPER: Global challenges facing plant pathology
###Global challenges facing plant pathology: multidisciplinary approaches to meet the food security and environmental challenges in the mid-twenty-first century### **May 2021** **Jeger M, Beresford R, Bock C, Brown N, Fox A, A. N, Vicent A, Xu X, Yuen J. 2021. [Global challenges facing plant pathology: multidisciplinary approaches to meet the food security and environmental challenges in the mid-twenty-first century.](https://cabiagbio.biomedcentral.com/counter/pdf/10.1186/s43170-021-00042-x.pdf) CABI Agriculture and Bioscience 2(20): 1-18. ** **ABSTRACT** In this review we emphasise, in particular: the multidisciplinary links between plant pathology and other disciplines; disease management, includ-ing precision agriculture, plant growth and development, and decision analysis and disease risk; the development and use of new and novel plant protection chemicals; new ways of exploiting host genetic diversity including host resistance deployment; a new perspective on biological control and microbial interactions; advances in surveillance and detection technologies; invasion of exotic and re-emerging plant pathogens; and the consequences of climate change affecting all aspects of agriculture, the environment, and their interactions. We draw conclusions in each of these areas, but in reaching forward over the next few decades, these inevitably lead to further research questions rather than solutions to the challenges we anticipate. **KEYWORDS** Plant pathology and multidisciplinary approaches; Disease management; Genetic diversity; Plant microbiome; Exotic plant pathogens and plant health; Climate change impacts;
RA4 PAPER: Spatial models guide restoration
###Using spatial models to identify refugia and guide restoration in response to an invasive plant pathogen### **October 2020** **McCarthy JK, Wiser SK, Bellingham PJ, Beresford RM, Campbell RE, Turner R, Richardson SJ. 2020. [Using spatial models to identify refugia and guide restoration in response to an invasive plant pathogen.](https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1365-2664.13756) Journal of Applied Ecology 58(1): 192-201. ** **ABSTRACT** To guide management and set priorities for conservation of at-risk species, areas of potential refugia where a Myrtaceae species is predicted to occur outside the pathogen range were identified under two myrtle rust distribution scenarios. Myrtle rust will thrive in New Zealand's warmer regions. Many native Myrtaceae are distributed within this area, but several species occur extensively outside the core range of the disease. Species distributed in cooler southern regions will be best placed to persist in refugia. Myrtaceae species with specific habitat requirements and narrow geographical ranges in warmer (northern) areas are likely to require ex situ or active in situ management. Even widely distributed species will benefit from the restoration of suitable habitat that supports multiple species outside the myrtle rust range. Synthesis and applications. Spatial data can be used to identify refugia and restoration opportunities, and thus inform landscape-level management responses to invasive pathogens. This approach can guide decisions over where to implement in situ (e.g. fungicide spraying) versus ex situ (e.g. seed banking, botanic gardens) management efforts. **KEYWORDS** eucalyptus rust; guava rust; invasive pathogens; *Lophomyrtus; Metrosideros;* myrtle rust; species distribution models; *Syzygium*
RA4 PAPER: Novel approaches in plant pathology
###Impact of novel methods and research approaches in plant pathology: Are individual advances sufficient to meet the wider challenges of disease management?### **May 2021** **Jeger M, Beresford R, Berlin A, Bock C, Fox A, Gold KM, Newton AC, Vicent A, Xu X. 2024. [Impact of novel methods and research approaches in plant pathology: Are individual advances sufficient to meet the wider challenges of disease management?](https://bsppjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/ppa.13927) Plant Pathology.** **ABSTRACT** Advances continue to be made by plant pathologists on topics in plant health, environmental protection and food security. Many advances have been made for individual crops, pathogens and diseases that in many cases have led to their successful management Applications of advanced techniques in epidemiological analysis based on spatial data, dynamic models and climatic variables have proved successful, as shown in an example for invasive populations of *Austropuccinia psidii* (see section 5.2, which was funded in part by Ngā Rākau Taketake's research theme Host, Pathogen and Environment). **KEYWORDS** artificial intelligence; diagnosis and surveillance; disease management; global change; microbiome; spatiotemporal spread
RA4 PAPER: NZ Myrtaceae susceptible to myrtle rust biotype
###New Zealand Myrtaceae are susceptible to a strain from the Eucalyptus biotype of Austropuccinia psidii present in South America### **January 2025** **Soewarto J, Pérez C, Bartlett M, Somchit C. Ganley B, Sutherland R, Simeto S, Stewart JE, Ibarra Caballero JR, Fraser S, Scott PM, Nadrajan J, Waipara N, Marsh A, Ryan J, Miller E, Smith GR. 2025. [New Zealand Myrtaceae are susceptible to a strain from the *Eucalyptus* biotype of *Austropuccinia psidii* present in South America](https://doi.org/10.1007/s10530-024-03465-5). Biol Invasions 27, 72, **ABSTRACT** The international spread of the myrtle rust pathogen, *Austropuccinia psidii*, can be largely attributed to the “pandemic” biotype that has more than 450 host species. However, within South America, the putative native range of *A. psidii*, multiple biotypes have been characterised, each with a restricted known number of hosts. These biotypes may pose a significant biosecurity threat to countries already affected by the pandemic biotype. Here, we report the susceptibility of four species of Myrtaceae from New Zealand, pōhutukawa (*Metrosideros excelsa*), mānuka (*Leptospermum scoparium*), kānuka (*Kunzea ericoides*), and rawiri mānuka (*Kunzea ericoides* ‘gumland ecotype’), to a strain of the *Eucalyptus* biotype of *A. psidii*. Symptoms and signs developed on inoculated plants of all species. Qualitative resistance phenotypes, with no disease development, were observed for all four species. However, no hypersensitive responses were observed. As seen for other biotypes, pōhutukawa had the greatest susceptibility, while kānuka had the lowest. These findings are consistent with prior work, showing that the *Eucalyptus* biotype can infect a broader range of species than its field host association implies. As well as uredinia (asexual spores), telia (sexual spores) developed on several plants, indicating that these species could provide a universal host for sexual reproduction and outcrossing between biotypes. Knowledge that the Eucalyptus biotype of *A. psidii* is virulent on several indigenous New Zealand Myrtaceae will inform future biosecurity risk assessments. These findings highlight the need to develop diagnostics tools to differentiate between biotypes and allow rapid responses to potential future incursions. **KEYWORDS** biological invasion; biosecurity risk assessment; disease resistance and susceptibility screening; host adaptation; pathogen virulence
###Weather associated with myrtle rust on the North Island east coast### **December 2020** **Beresford R, Sutherland R. 2020. Weather associated with myrtle rust on the North Island east coast. 6 p. ** **ABSTRACT** The aim of this study was to use a modelling approach to examine winter temperatures in New Zealand, particularly on the east coast of the North Island, and to identify areas where temperatures are favourable for infection during winter and areas where the pathogen remains in the latent phase. Latent overwintering is considered to occur when the latent period takes at least one month (30 days) to complete, i.e., when one or fewer latent periods occur per month. If the latent period is less than one month (more than one latent period occurring per month), it is considered that the infection cycle continues through winter.
The Myrtle Rust Risk Prediction platform was built by HortPlus and combines weather data from a national network of weather stations in key areas. The data feed into a model developed by Dr Robert Beresford at Plant & Food Research to generate local predictions of myrtle rust risk. This platform is freely available to all — tangata whenua, the nursery industry, conservation groups, myrtle rust researchers and the public — to help determine the risk for myrtle rust based on local weather conditions. For further information please see: [Myrtle Rust Risk Prediction - a new data platform](https://bioheritage.nz/myrtle-rust-risk-prediction-a-new-data-platform/)
RA4 PRESENTATION: Assessing myrtle rust climatic risk
### A versatile model for assessing climatic risk of myrtle rust### **June 2023** **Beresford R. 2023. A versatile model for assessing climatic risk of myrtle rust. Australasian Myrtle Rust Conference, Sydney, Australia, 21-24 June 2023.** **ABSTRACT** A versatile model for assessing climatic risk of myrtle rust.
RA5 PAPER: Phytophthora agathidicida genome
###Chromosome-level assembly of the *Phytophthora agathidicida* genome reveals adaptation in effector gene families### **November 2022** **Cox M, Guo Y, Winter D, Sen D, Cauldron N, Shiller J, Bradley E, Ganley A, Gerth M, Lacey R, McDougal R, Panda P, Williams N, Grunwald N, Mesarich C, Bradshaw R. 2022. [Chromosome-level assembly of the *Phytophthora agathidicida* genome reveals adaptation in effector gene families](https://www.frontiersin.org/articles/10.3389/fmicb.2022.1038444/pdf?isPublishedV2=False"). Frontiers in Microbiology 13. ** **ABSTRACT** A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. This is the first *Phytophthora* genome assembled to chromosome level, and additional effector gene analysis was undertaken. Further analysis of this complete genome assembly will help inform new methods of disease control against *P. agathidicida* and other *Phytophthora* species, ultimately helping decipher how *Phytophthora* pathogens have evolved to shape their effector repertoires and how they might adapt in the future. **KEYWORDS** *Phytophthora*, oomycete, kauri dieback, forest disease, chromosome-level genome assembly, chromatin conformation capture, effectors
RA5 PAPER: Genomic analysis of 31 Phytophthora genomes
###Comparative genomic analysis of 31 *Phytophthora* genomes reveal genome plasticity and horizontal gene transfer### **January 2022** **Kronmiller BA, Feau N, Shen D, Tabima JF, Ali SS, Armitage AD, Arredondo FD, Bailey BA, Bollmann SR, Dale A, Harrison R, Hrywkiw K, Kasuga T, McDougal R, Nellist CF, Panda P, Tripathy S, Williams NM, Ye W, Wang Y, Hamelin RC, Grunwald NJ. 2022. [Comparative genomic analysis of 31 *Phytophthora* genomes reveal genome plasticity and horizontal gene transfer.](https://apsjournals.apsnet.org/doi/epdf/10.1094/MPMI-06-22-0133-R) Molecular Plant-Microbe Interactions.** **ABSTRACT** The *Phytophthora* genus includes over 180 known species, infecting a wide range of plant hosts including crops, trees, and ornamentals. This paper examines the sequencing of 31 individual *Phytophthora* species genomes and 24 individual transcriptomes to study genetic relationships across the genus. **KEYWORDS** effectors; horizontal gene transfer; oomycete plant pathogens; *Phytophthora*
###Plant-pathogen management in a native forest ecosystem### **June 2023** **Mainwaring JC, Vink JNA, Gerth ML. 2023. [Plant-pathogen management in a native forest ecosystem](https://www.sciencedirect.com/science/article/pii/S0960982223001872/pdfft?md5=86e31c8b5fe41c6b536b7ad075471b9a&pid=1-s2.0-S0960982223001872-main.pdf). Current Biology 33(11): R500-R505.** **ABSTRACT** Forest ecosystems all over the world are facing a growing threat from plant-disease outbreaks. As pollution, climate change, and global pathogen movement intensify, so too do the impacts of forest pathogens. In this essay, we examine a case study of the New Zealand kauri tree (Agathis australis) and its oomycetepathogen, Phytophthora agathidicida. We focus on the interactions between the host, pathogen, and environment — the building blocks of the ‘disease triangle’, a framework used by plant pathologists to understand and manage diseases. We delve into why this framework is more challenging to apply to trees than crops, taking into account the differences in reproductive time, level of domestication, and surrounding biodiversity between the host (a long-lived native tree species) and typical crop plants. We also address the difficulties in managing Phytophthora diseases compared to fungal or bacterial pathogens. Furthermore, we explore the complexities of the environmental aspect of the disease triangle. In forest ecosystems, the environment is particularly complex, encompassing diverse macro- and microbiotic influences, forest fragmentation, land use, and climate change. By exploring these complexities, we emphasize the importance of targeting multiple components of the disease triangle simultaneously to make effective management gains. Finally, we highlight the invaluable contribution of indigenous knowledge systems in bringing a holistic approach to managing forest pathogens in Aotearoa New Zealand and beyond. **KEYWORDS** Plant pathogens, damage, forest ecosystems, research, management, *Phytophthora*, kauri dieback, indigenous knowledge
###*Austropuccinia psidii*, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements.### **March 2020** **Tobias PA, Schwessinger B, Deng CH, Wu C, Dong C, Sperschneider J, Jones A, Lou Z, Zhang P, Sandhu K, Smith GR, Tibbits J, Chagné D, Park RF. 2020. [*Austropuccinia psidii*, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements.](https://academic.oup.com/g3journal/article-pdf/11/3/jkaa015/46043700/jkaa015.pdf) G3 Genes|Genomes|Genetics 11(3): 16. ** **ABSTRACT** *Austropuccinia psidii*, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. *A. psidii* has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into *A. psidii* pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. **KEYWORDS** myrtle rust, Pucciniomycotina, fungal genome evolution, Myrtaceae, transposable elements
###Harnessing CRISPR-Cas for oomycete genome editing### **September 2023** **Vink JNA, Hayhurst M, Gerth ML. 2023. [Harnessing CRISPR-Cas for oomycete genome editing.](https://www.sciencedirect.com/science/article/pii/S0966842X23000975/pdfft?md5=2b45356e7ceaf512f9ea29c79637679f&pid=1-s2.0-S0966842X23000975-main.pdf) Trends in Microbiology 31(9): 947 - 958. ** **ABSTRACT** Advances in CRISPR-Cas technologies (a genome editing tool) are being used to illuminate the biology of oomycetes, which ultimately can guide the development of tools for managing oomycete diseases. This paper also discusses some of the challenges to applying CRISPR-Cas in oomycetes and potential ways to overcome them. **KEYWORDS** CRISPR; genome editing; oomycetes; *Phytophthora*; stramenopiles
RA6 POSTER: How A. psidii infects mānuka causing myrtle rust
###How does *Austropuccinia psidii* infect mānuka to cause myrtle rust? ### **November 2022** **Frampton R_, Smith G, Shuey L, Degnan R, Johns T, Gilkes J, Currie M, Sullivan J, David C, Pringle G, Kalamorz F, Addison S, Marsh A, Chagné D, Hilario Andrade E, Wu C, Templeton M, McTaggart A, Eccersall S, Meisrimler C, Dobson R, Pegg G. 2022. How does *Austropuccinia psidii* infect mānuka to cause myrtle rust? New Zealand Microbiology Society Meeting. Wellington, 21 - 24 November 2022. ** **ABSTRACT** Generally, rust fungi are specialised plant pathogens with highly specific host ranges. However, the pandemic biotype of *Austropuccinia psidii* (the causative agent of myrtle rust disease) has a current host range of almost 500 known Myrtaceae species. This host range is exceptional, and potentially unique. *A. psidii* infects *Leptospermum scoparium* (mānuka) as well as many other New Zealand native plants. Effectors and CAZymes are known to be key components during rust infection processes. The expression levels of effectors and CAZymes were measured over time following inoculation of mānuka plants to understand how *A. psidii* causes myrtle rust.
RA6 POSTER: A. psidii effector protein role
###Elucidating the Role of an *Austropuccinia psidii* Effector Protein During Myrtle Rust Infection### **February 2024** **Sullivan J, Currie M, Eccersall S, Gilkes J, Frampton R, Panjikar S, Sethi A, Meisrimler C, Smith G, Dobson R. 2024. Elucidating the Role of an *Austropuccinia psidii* Effector Protein During Myrtle Rust Infection. 49th Lorne Conference on Protein Structure and Function. Lorne, Victoria, Australia. 4 - 8 Feb 2024. ** **ABSTRACT** Myrtle rust is caused by the invasive fungus *Austropuccinia psidii* and is incredibly infectious and physically devastating to Myrtaceae plants. The disease was first detected in New Zealand in 2017 and continues to spread rapidly across the country. The presence of the disease in Australia has already caused major declines in Myrtaceae populations (e.g., eucalyptus in Queensland) and now threatens Aotearoa-New Zealand natives, including taonga species such as pōhutukawa, mānuka and rātā. Localised extinctions of myrtle plants have already begun to occur in Aotearoa. Transcript experiments have identified several proteins expressed during the first 24-48 hours of infection by *A. psidii* on mānuka. This expression pattern is a signature of their important role in the successful infection of plant cells. In other plant pathogens these ‘effector proteins’ are known to manipulate the host plant’s cellular processes to boost pathogen fitness. Here, our aim is to elucidate the role of the *A. psidii* effector protein, AP1260, during infection through bioinformatic and biophysical analysis. Sequence homology and predictions of AP1260’s structure and cellular localisation were made and used to compare to later biophysical analysis. Biophysical studies sought to determine its physical characteristics in solution. These included analytical ultracentrifugation, fluorescence spectroscopy, circular dichroism, small-angle X-ray scattering, and nuclear magnetic resonance. Functional analysis of AP1260 used agrobacterium-mediated transformation of *N. benthamiana* and yeast-two-hybrid to determine its localisation and in planta interaction partners. The results obtained in this study represent the first studies of an *A. psidii* effector protein. Characterisation of AP1260 improves the knowledge of the mechanisms of *A. psidii* infection and may uncover methods to interfere with its function, making its characterisation critical to the biosecurity of nations with Myrtaceae populations. The outcomes of this research may lead to the development of a novel and effective method to treat and control myrtle rust.
RA6 POSTER: Defining AP5292 effector protein role
###Defining the role of novel fungal effector protein AP5292 during myrtle rust infections to inform management of *Austropuccinia psidii*### **June 2023** **Hambrook N, Sullivan J, Currie M, Eccersall S, Ogilvie S, Gilks J, Johns T, Meisrimler C, Smith G, Dobson R. 2023. Defining the role of novel fungal effector protein AP5292 during myrtle rust infections to inform management of *Austropuccinia psidii*. Australasian Myrtle Rust Conference. Sydney, Australia. 21 - 23 June 2023. **
RA6 THESIS: Structure and function of A. psidii effector proteins
###The structure and function of effector proteins expressed by *Austropuccinia psidii* in the early stages of myrtle rust infection### **2021** **Johns T. 2021. The structure and function of effector proteins expressed by *Austropuccinia psidii* in the early stages of myrtle rust infection. Unpublished Honours thesis, University of Canterbury. 46 p. ** **NOTE** This thesis has been rewritten in a manuscript format and co-authored by Grant Smith, Rebekah Frampton, Falk Kalamorz, Michael Currie, Jenna Gilkes, Claudia Meisrimler and Renwick Dobson. **ABSTRACT** Myrtle rust disease, caused by the fungal rust pathogen *Austropuccinia psidii*, has been known to infect a wide range of Myrtaceae hosts. In Australia, the disease has caused the population of Myrtaceae plants to decline, and threatens to do the same to beloved New Zealand natives. Despite the large host range of *A. psidii*, many aspects about the infection process are still unknown. It is hypothesised that like many other pathogens, effector proteins play a significant role in establishing a successful infection in the host. This research reports the identification of five novel *A. psidii* effector proteins that are predicted to be essential in the establishment of myrtle rust infection. These effector proteins are the first to be studied from *A. psidii*. Structural features were identified on *A. psidii* effector candidates using bioinformatics and analytical methods. Bioinformatics show that two of these proteins are similar to fungal cellulase and xyloglucanase enzymes. One effector protein, AP1260 was successfully expressed and purified by recombinant expression in *E. coli* cells. AP1260 is a monodisperse protein as shown by analytical ultracentrifugation experiments and contains secondary structures as shown by circular dichroism. Emphasis was put on obtaining X-ray crystallography data on AP1260 to probe its biochemical function in myrtle rust infection, however further crystallography screening is required. Understanding the structure and mode of action of these effectors is crucial in order to provide insight into the establishment and progression of myrtle rust. Therefore, it is crucial to further probe these effectors as they are potential targets for a disease management strategy for myrtle rust disease. **KEYWORDS** Bioinformatics; APSIP001; APSIP005; Effector; Proteins; SWISS-MODEL; AlphaFold2; X-ray crystallography; Enzymes; Homology
RA6 THESIS: Characterising Effector Protein AP1260
###Characterising Effector Protein, AP1260, of the Myrtle Rust Causing *Austropuccinia psidii*### **2022** **Sullivan J. 2022. Characterising Effector Protein, AP1260, of the Myrtle Rust Causing *Austropuccinia psidii*. Unpublished BSc honours thesis, University of Canterbury. 54 p. ** **ABSTRACT** __Significance__ Myrtle rust is caused by the invasive fungus *Austropuccinia psidii* and is incredibly infectious and physically devastating to Myrtaceae plants. The pandemic biotype of the disease has spread across five continents and was first detected in New Zealand in 2017. The presence of the disease in Australia has already caused major declines in Myrtaceae populations (e.g., eucalyptus) and now threatens New Zealand natives, including taonga species such as pōhutukawa, mānuka and rātā. __Rationale__ Transcriptomics by collaborators at Plant and Food Research identified several proteins that are expressed in the early stages of *A. psidii* infection of mānuka—a signature that they are important for the infection of plant cells. In other fungi, these ‘effector proteins’ are known to manipulate the host plants cellular processes. My research focuses on one of these effector proteins, AP1260. The aim is to define the characteristics of AP1260 through bioinformatic and biophysical analysis. __Results__ The results obtained in this study represent the first studies of an *A. psidii* effector protein. Characteristics such as mass, dynamics, stability, and shape of AP1260 were determined. This led to the discovery of a potentially intrinsically disordered region within AP1260. __Conclusions__ Characterisation of AP1260 will vastly improve the knowledge of the mechanisms of *A. psidii* infection and may uncover methods to interfere with its function, making its characterisation critical to the biosecurity of nations with Myrtaceae populations. The outcome of this research will be critical for developing methods for controlling and potentially preventing myrtle rust disease.
RA6 PRESENTATION: Understanding early A. psidii - manuka interaction
###Transcript to protein: understanding the early pathology of the *Austropuccinia psidii* - mānuka interaction### **June 2023** **Frampton R, Shuey L, Degnan R, Gilkes J, Johns T, Currie M, Sullivan J, Hambrook N, David C, Pringle G, Kalamorz F, Addison S, Chagné D, Eccersall S, Meisrimler C, Dobson R, Pegg G, Smith G, . 2023. Transcript to protein: understanding the early pathology of the *Austropuccinia psidii* - mānuka interaction. Australasian Myrtle Rust Conference, Sydney, Australia, 21 - 23 June 2023.** Presented by Rebekah Frampton.
RA6 PRESENTATION: Targeting A. psidii effectors
###Targeting *Austropuccinia psidii* effectors.### **February 2021** **Smith G, Dobson R, Meisrimler C, Frampton C, Kalamorz F, David C, Chagné D, Shuey L, Gilkes J, Johns T. 2021. Targeting *Austropuccinia psidii* effectors. Myrtle Ora Community Meeting.** **ABSTRACT** A presentation by Grant Smith on research from Ngā Rākau Taketake's Theme 6: Host Pathogen and Environment, given to the Myrtle Ora Community Meeting 02/02/2021.
RA6 PRESENTATION: Understanding a taonga killer
###Understanding a taonga killer: how does Austropuccinia psidii cause myrtle rust?### **May 2023** **Smith G. 2023. Understanding a taonga killer: how does *Austropuccinia psidii* cause myrtle rust? Kaurilands Summit Whangārei, New Zealand, 11/05/2023.** Presented as part of the Kaurilands Summit 2023, hosted by Ngā Rākau Taketake.
MR BIOLOGY PAPER: Resistance to Austropuccinia psidii
###Resistance of New Zealand Provenance *Leptospermum scoparium, Kunzea robusta, Kunzea linearis*, and *Metrosideros excelsa* to *Austropuccinia psidii*### **April 2020** **Smith GR, Ganley BJ, Chagné D, Nadarajan J, Pathirana RN, Ryan J, Arnst EA, Sutherland R, Soewarto J, Houliston G, Marsh AT, Koot E, Carnegie AJ, Menzies T, Lee DJ, Shuey LS, Pegg GS. 2020. [Resistance of New Zealand Provenance *Leptospermum scoparium, Kunzea robusta, Kunzea linearis*, and *Metrosideros excelsa* to *Austropuccinia psidii*.](https://apsjournals.apsnet.org/doi/epdf/10.1094/PDIS-11-19-2302-RE) Plant Disease 104(6): 1771-1780. ** **ABSTRACT** This paper reports the first assessments of germplasm from six myrtaceous species— *Meterosideros excelsa* (pōhutukawa), *Leptospermum scoparium* (mānuka), *Kunzea robusta* (kānuka), *Kunzea linearis* (rawiri mānuka), *Lophomyrtus bullata* (ramarama), and *Lophomyrtus obcordata* (rōhutu)—of New Zealand provenance for resistance to the pandemic strain of *Austropuccinia psidii*, and discuss the findings in the context of options to maintain these species within ecosystems. **KEYWORDS** cultivar resistance; disease development and spread; disease management; epidemiology; fungi; kānuka; mānuka; myrtaceae; ornamentals; pandemic strain; pōhutukawa; ramarama; rawiri mānuka; rōhutu; trees; woody ornamentals
MR BIOLOGY PAPER: Susceptibility of native New Zealand Myrtaceae
###Susceptibility of native New Zealand Myrtaceae to the South African strain of *Austropuccinia psidii*: A biosecurity threat### **November 2020** **Soewarto J, Somchit C, du Plessis E, Barnes I, Granados GM, Wingfield MJ, Shuey L, Bartlett M, Fraser S, Scott P, Miller E, Waipara N, Sutherland R, Ganley B. 2021. [Susceptibility of native New Zealand Myrtaceae to the South African strain of *Austropuccinia psidii*: A biosecurity threat.](https://bsppjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/ppa.13321) Plant Pathology 70(3): 667-675. ** **ABSTRACT** *Austropuccinia psidii*, cause of myrtle rust, has spread globally where Myrtaceae occur. Multiple strains of *A. psidii* have been identified, including a unique strain found only in South Africa. The South African strain is a biosecurity concern for species of Myrtaceae worldwide. This is because preliminary testing of South African Myrtaceae suggests it could have a wide host range, and thus has the potential to be invasive. In this study, we assessed the ability of the South African strain to infect other species of Myrtaceae by testing the susceptibility of New Zealand provenance Myrtaceae. Seedlings of four native New Zealand Myrtaceae species (*Metrosideros excelsa, Leptospermum scoparium, Kunzea robusta*, and *Kunzea linearis*) were artificially inoculated in South Africa with a single-uredinium isolate of the South African strain. Fourteen days after inoculation, uredinia, and in many cases telia, had developed on the young leaves and stems of all four host species, which led to shoot tip dieback in the more severe cases. When comparisons were made between the species, *K. robusta* was the least susceptible to the South African strain of* A. psidii*, while *L. scoparium* and *M. excelsa* were the most susceptible. While only a limited number of seed families were tested, only a small proportion of the seedlings showed resistance to infection by the South African strain. This preliminary testing highlights the potential invasive risk the South African strain poses to global Myrtaceae communities, including New Zealand Myrtaceae. **KEYWORDS** Artificial inoculation; biosecurity; Eucalyptus rust; guava rust South African strain
MR BIOLOGY REPORT: Myrtaceae vulnerability
###Vulnerability of New Zealand Myrtaceae species to natural infection by *Austropuccinia psidii* (myrtle rust) **October 2021** **Beresford R, Soewarto J, Somchit C, Hasna L, Ramos Romero L. 2021. Vulnerability of New Zealand Myrtaceae species to natural infection by *Austropuccinia psidii* (myrtle rust). PFR SPTS No. 21702. https://doi.org/10.34721/1v1s-qz14** **ABSTRACT** Current knowledge about the vulnerability of New Zealand’s native myrtle species to *A. psidii* comes from resistance screening of young seedlings performed with artificial inoculation under controlled conditions, from surveillance data collected during the initial incursion response and from field observations. The controlled resistance screening is important because it can potentially reveal the inherent genetic susceptibility of species, whereas surveillance data and field observations may reflect sampling bias and other factors affecting vulnerability, such as presence of new shoot growth, presence of airborne spores (inoculum) and suitability of weather conditions. However, it needs to be determined how well the method of screening young seedlings under artificial conditions represents the effects of myrtle rust on host species in the natural environment. This research established field trials in Rotorua and Auckland in spring 2019 to compare the artificial inoculation results with myrtle rust development at two sites where inoculum and environmental conditions were relatively uniform. Each trial contained five New Zealand native Myrtaceae species: ramarama (*Lophomyrtus bullata*), rōhutu (*Lophomyrtus obcordata*) pōhutukawa (*Metrosideros excelsa*), mānuka (*Leptospermum scoparium*) and kānuka (*Kunzea robusta*) and the exotic species, rose apple (*Syzygium jambos*), which is highly susceptible worldwide and was included to provide an international comparison.
MR BIOLOGY VIDEO: Myrtle rust field susceptibility trials
###Myrtle rust field susceptibility trials### **2020** **BioHeritage Challenge. 2020. Myrtle rust field susceptibility trials. YouTube. ** **ABSTRACT** This project aimed to assess the risk posed by myrtle rust to six Myrtaceae species under natural New Zealand conditions. Dr Julia Soewarto (Scion) and Dr Rob Beresford (Plant & Food Research) explain how they're finding out which of our native species are most vulnerable to this deadly disease. To find out more about their research, visit [https://bit.ly/2ZmuOQ5](https://bit.ly/2ZmuOQ5)
MR BIOLOGY WEBINAR: Predicting future spread
###Predicting future spread of myrtle rust in Aotearoa New Zealand### **September 2021** **Beresford R. 2021. Predicting future spread of myrtle rust in Aotearoa New Zealand. Beyond Myrtle Rust Webinar Series. ** **ABSTRACT** Myrtle rust is here to stay and continues to spread within Aotearoa, with devastating impacts on some species. It has been recorded in most North Island regions, although is still arriving at new localities within these regions. It is spreading more slowly in the South Island, but has already established further south than initially expected. Epidemiological concepts developed for other rust pathogens can help us to understand spatio-temporal spread for myrtle rust. Key parameters are wind, host susceptibility, host density and climatic suitability. Join us for this presentation by plant pathologist Rob Beresford where he will examine the dynamics of spread and consider surveillance requirements, early detection in new localities and the use of climatic risk predictions.
MR BIOLOGY WEBINAR: Monitoring Austropuccinia psidii impact
###Monitoring the impact of *Austropuccinia psidii* on native Myrtaceae in the ngahere### **August 2021** **Sutherland R. 2021. Monitoring the impact of *Austropuccinia psidii* on native Myrtaceae in the ngahere. Beyond Myrtle Rust Webinar Series. 11/08/2021** **ABSTRACT** Since the arrival of myrtle rust in May 2017 to Aotearoa, the fungus responsible for the disease (*Austropuccinia psidii*) has spread across all regions of Te Ika-a-Māui, the North Island and parts of Te Waka-o-Māui, the South Island. The disease impacts native and non-native Myrtle species in urban areas and the ngahere (forest). Rōhutu and ramarama (Lophomyrtus spp.) are among our most susceptible species with severe infection recorded on leaves, stems, flowers, fruit and in some cases, death of seedlings and mature trees. Regeneration of these species is likely to be negatively impacted and localised extinction possible. Long term monitoring plots were established in 2018 in the Bay of Plenty region, in an area where a variety of different myrtle species naturally occur including ramarama, rōhutu, mānuka, climbing rātā and pōhutukawa. Mature trees and seedlings are monitored fortnightly for disease severity and extent within the area. Data from this monitoring show that disease impacts have increased over the past three summers, possibly due to increasing myrtle rust inoculum load in the environment. Ecosystem impacts from myrtle rust extend beyond plant loss. In forests across New Zealand, where Myrtaceae are present, the loss of these species could have severe consequences on invertebrate and vertebrate communities, highlighting the cascading environmental impacts to forest ecosystems. Surveillance and monitoring will play a critical role in identifying ecosystems and populations at risk.
REPORT: Optimising methods for screening MR susceptible hosts
###Optimising methods for screening the susceptibility of host species populations to myrtle rust### **July 2022** **Dobbie K, Bartlett M, Lloyd A, Waller L. 2022. Optimising methods for screening the susceptibility of host species populations to myrtle rust. 16 p. https://doi.org/10.34721/H84C-R389** **ABSTRACT** The highly invasive rust *Austropuccinia psidii* (myrtle rust) has an unusually large host range, with over 480 known hosts worldwide. The aim of this project is to carry out a pilot study to develop a fast, efficient, and cost-effective method that can screen plants for susceptibility to myrtle rust within any laboratory with a PC1 microorganism facility with MPI approval. Four methods were trialled, rooted cuttings, cut material in Ellepots, cut material in water agar (WA) in sealed jars and in WA in open falcon tubes. The cut material was inoculated within 24 hours of collection with the exception of the rooted cuttings. Rooted cuttings showed good results, however the method to set cuttings for this group of hosts needs to be investigated further to speed up the development of roots and new flush. Health of the cut material in Ellepots and WA in open falcon tubes deteriorated to a point where there was not enough healthy tissue to sustain myrtle rust infection in most cases, however some results were obtained from the former. The cut material set in WA in sealed jars showed promising results and warrants further investigation to optimise the health of the cuttings over time. Good infection rates were obtained using misting tents with humidity controllers. This means that these trials can be carried out in any PC1 microorganisms facility without the need for environmentally controlled chambers/rooms.
POSTER: Host Pathogen & Environment, Kaurilands 2023
###Host, Pathogen & Environment### **May 2023** **ABSTRACT** Looking at the role of environmental factors play on disease expression and severity, pathogen spread and establishment, as well as investigating plant pathogen genomes. Poster shared at the Kaurilands Summit 2023
VIDEO: Myrtle rust monitoring in Rotorua
###Myrtle rust monitoring in Rotorua### **May 2020** **ABSTRACT** We’re in the field with Roanne Sutherland from Scion, talking about monitoring myrtle rust. This plant pathogen arrived in Aotearoa in 2017 and has been infecting plants ever since. We need to monitor its progress throughout the country if we have any chance of winning the fight to save our native species. For more information on myrtle rust in New Zealand go to: View the Myrtle Ora topic on our website. https://www.myrtlerust.org.nz/ https://www.myrtlerust.org.nz/science…
VIDEO: Host, Pathogen & Environment 2022
###Host, Pathogen & Environment 2022 **June 2022** **Akariro Films. 2022. Host, Pathogen and Environment - Video for Kaurilands Summit 2022. YouTube, BioHeritage Challenge. ** **ABSTRACT** The ‘Host, Pathogen and Environment’ team is focusing on the ‘disease triangle’: host susceptibility, the pathogen and the right environment for disease expression. They are investigating the role environmental factors play on kauri dieback and myrtle rust disease expression and severity, as well as researching the pathogen genomes. The knowledge they gain will contribute to improving surveillance, control, management and conservation efforts, and they hope to discover new ways to mediate these diseases. Click 'play' to view what they've been up to in the first three years of the programme. This video directed by Ngāriki Ngatae (Akaririo Films) was screened at the online Kaurilands Summit 2022. This research programme is funded by Ngā Rākau Taketake, which is administered by New Zealand's Biological Heritage National Science Challenge | Ngā Koiora Tuku Iho.