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The Department of Pest Management and Conservation carries out research and teaching in the following specialist areas: Animal behavior; Conservation and biodiversity; Ecological restoration; Evolutionary biology; Fire ecology; Molecular ecology; Plant microbiology; Plant pathology; Remediation of degraded and contaminated land; Soil ecology; Sustainable agriculture and ecosystem services; Wildlife and pest management.
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Item Open Access Networks of risk: International tourists as a biosecurity pathway into national parks(Springer Nature, 2024-12) Hulme, PhilipInternational tourists are recognised as vectors of alien microbes, plants, and animals into protected areas worldwide, either by introducing species from overseas or redistributing alien species within a region. Quantitative estimates of the risk from this introduction pathway have relied on surveys of invasive alien species associated with tourist clothing or transport vectors. In contrast, the large-scale movement of tourists across multiple protected areas within a region has rarely been examined. The New Zealand International Visitor Survey was used to estimate the frequency with which several thousand international travellers visited the nation’s 13 national parks. Trends in international visitor movements were compared immediately prior to the closure of international borders due to the SARS-CoV-2 pandemic and again once the border had reopened. Approximately one-third of international visitors only visited a single national park but over 20% visited five or more. The long tail in the frequency of national parks visited highlights that a small number of tourists pose a greater risk of introducing or moving invasive alien species among different protected areas. European tourists visited more national parks and were more likely to camp or stay in mountain huts while in New Zealand, potentially posing a greater biosecurity risk than other nationalities. The largely montane nature of most national parks imposes a strong bioclimatic filter on alien species establishment and combined with border controls, suggests international tourists pose a greater risk by disseminating already established alien species more widely among and within national parks. Network analyses highlighted geographic clustering of national parks based on tourist movements that might facilitate regional spread of alien species. Greater investment in the education of international tourists about the biosecurity risks they pose through spreading alien species into national parks is needed to address Target 6 of the Global Biodiversity Framework.Item Open Access Damage costs from invasive species exceed management expenditure in nations experiencing lower economic activity(Elsevier, 2024-06) Bradshaw, CJA; Hulme, Philip; Hudgins, EJ; Leung, B; Kourantidou, M; Courtois, P; Turbelin, AJ; McDermott, SM; Lee, K; Ahmed, DA; Latombe, G; Bang, A; Bodey, TW; Haubrock, PJ; Saltré, F; Courchamp, FWhile data on biological invasions and their economic toll are increasingly available, drivers of susceptibility to damage and cost-effectiveness of management in reducing long-term costs remain poorly understood. We used data describing the damage costs of, and management expenditure on, invasive species among 56 nations between 2000 and 2020 reported in the InvaCost database to test the overarching hypothesis that higher-income nations and those with higher trade volume have a higher efficiency to limit the damage incurred by invasive species by spending relatively more on management. We also tested whether nations with (i) more corruption have a reduced capacity to manage invasive species, leading to relatively higher damage costs, (ii) more educated citizens or greater technological and scientific output allow for improved incentives and ability to manage invasive species, thereby reducing relative damage costs, and (iii) economies based on higher primary resource dependencies (e.g., agriculture) are at greater risk of incurring high costs of invasive species, and so all other conditions being equal, have higher relative damage costs compared to management expenditure. By focusing on the ratio between damage costs and management expenditure, we analyse the willingness of countries to invest in management as a function of the extent of the damage suffered. We show that economic activity, measured by the volume of trade, is the main determinant of this ratio — the greater the volume, the smaller the ratio. We also found a higher rate of increase in the damage:management ratio as a country's proportion of total land area devoted to agriculture increased, suggesting that a higher economic dependency on agriculture predisposes a country to greater damage costs from invasive species over time. When considering the proportion of total costs identified as damage-related, results indicated that higher government investment in education produced higher proportional damage, and lower corruption and lower trade volume both reduced proportional damage. Our overall results suggest that wealthier nations with high per-capita imports of goods and services are more susceptible to damage, but also have a greater capacity to reduce it, and are therefore less threatened by biological invasions than countries with fewer resources and lower imports.Item Open Access Dolomedes fishing spider biology: Gaps and opportunities for future research(Frontiers Media, 2024-11-25) Yu, Kuang-Ping; Roithmair, Zita; Kurovski, Jillian; Connolly, Simon J; Vink, Cornelis; Johnson, James Chadwick; Kralj-Fišer, Simona; Kuntner, Matjaž; Hebets, Eileen A; Painting, Christina JDolomedes may easily be considered to be among the most charismatic spider taxa. Known colloquially as fishing or raft spiders, this clade of dolomedid cursorial hunters is speciose with about 100 valid species names. Most Dolomedes are large spiders that inhabit water bodies across all continents except Antarctica and, interestingly, South America. Dolomedes have captured the attention of researchers and the public alike for their ability to walk on and submerge under water, fish for prey (including small vertebrates), and for their often-bizarre mating behavior that includes examples of male spontaneous death and sexual cannibalism. In this review, we critically evaluate what is known of Dolomedes biology, focusing on their systematics and morphology, ecology, behavior, and conservation. Given their close association with water, Dolomedes may be particularly vulnerable to the impacts of anthropogenic change and provide an important group of indicator species for understanding the effect of pollution, habitat loss and climate change. We outline a roadmap for future studies that, in our view, will consolidate Dolomedes as an ideal model lineage among spiders for addressing a vast array of questions across multiple fields of biology.Item Open Access In vitro inhibition of Sclerotinia sclerotiorum mycelial growth and reduction of sclerotial viability by the volatile bioactive compounds of Brassicaceae crops(Oxford University Press, 2023-12) Dassanayaka, MP; Casonato, Seona; Jones, ElizabethAims: Sclerotinia sclerotiorum is an important pathogen of a wide range of crops, with current control mostly relying on the use of fungicides. This study assessed the effect of biofumigation on in vitro inhibition of mycelial growth and reduction of sclerotial viability of S. sclerotiorum as an attempt to seek an alternative management strategy. Methods and results: The effect of different biofumigant crop types to inhibit mycelial growth of ten S. sclerotiorum isolates was investigated, with Brassica juncea 'Caliente 199' being the most effective biofumigant crop. The efficacy of 'Caliente 199' to inhibit mycelial growth and reduce sclerotial viability was influenced by different crop factors. Plant tissue of 'Caliente 199' harvested at 50% or 100% flowering and adjusted to 80% (w/w) moisture resulted in greater mycelial inhibition and a reduction in the sclerotial viability compared with the vegetative tissue with the same plant moisture. Mycelial inhibition and reduction of sclerotial viability were affected by tissue quantity. Whole plant tissue and shoots only resulted in a similar inhibition of mycelial growth, but whole plant tissue resulted in a greater reduction of sclerotial viability. The S. sclerotiorum isolates differed in sensitivity to the volatile bioactive compounds released by the biofumigant plant tissue. Conclusions: The volatile bioactive compounds released by 'Caliente 199' resulted in effective mycelial inhibition but did not kill sclerotia completely.Item Open Access Pathogenicity and virulence-associated factors of Pseudomonas syringae pv. syringae and [P. amygdali pv. morsprunorum] strains from New Zealand sweet cherry (Prunus avium) orchards(Wiley-Blackwell, 2024-09) Marroni, M Virginia; Casonato, Seona; Visnovsky, Sandra B; Pitman, Andrew R; Beresford, Robert M; Jones, ElizabethPreviously genetically characterised strains of Pseudomonas syringae. pv. syringae (Pss), [P. amygdali pv. morsprunorum] (Pam, syn. P. s. pv. morsprunorum race 1) and Pseudomonas spp. from New Zealand were characterised for their pathogenicity and ag-gressiveness in plant tissue and associated virulence factors. Lesions on detached, Pss-inoculated immature fruit increased rapidly in size and, at 10 days post inoculation (dpi), had larger areas under the disease progress curve (AUDPC) than Pam-inoculated fruit (48.9 and 22.0, respectively). Detached leaves infiltrated with Pss-developed symptoms within 1 dpi and from 2 dpi for Pam. Necrosis from most Pss strains extended into the leaf veins by 7 dpi, while Pam strains' necrosis was confined to the inoculation site. On detached 1-year-old cherry shoots, Pseudomonas spp. strains exhibited the smallest mean lesion size (2.1–2.4 mm), whereas larger mean lesion sizes were observed with Pss strains (5.7–13.7 mm) and Pam strains (3.9–14.0 mm). A functional T3SS was inferred for Pss and Pam strains based on the hypersensitivity reactions observed on tobacco leaves and symptoms elicited on cherry tissue. Syringomycin production was prevalent (88%) among Pss strains. In contrast, only 1.4% of Pam strains produced coronatine. Most Pss strains (97.0%) were able to catalyse ice formation. The coexistence of strains with varying degrees of virulence and non-pathogenic strains suggests a complex ecological balance, where multiple factors, including genetic variation, virulence traits and environmental conditions, shape the population dynamics and disease outcomes.Item Open Access Physiological stage drives fungal community dynamics and diversity in Leptospermum scoparium (mānuka) flowers(John Wiley & Sons Ltd., 2023-03) Larrouy, JL; Dhami, MK; Jones, Elizabeth; Ridgway, HJFlowers are an important niche for microbes, and microbes in turn influence plant fitness. As flower morphology and biology change rapidly over time, dynamic niches for microbes are formed and lost. Floral physiology at each life stage can therefore influence arrival, persistence and loss of microbial species; however, this remains little understood despite its potential consequences for host reproductive success. Through internal transcribed spacer 1 (ITS1) community profiling, we characterized the effect of transitioning through five floral stages of mānuka (Leptospermum scoparium), from immature bud to spent flower, and subsequent allocation to seed, on the flower-inhabiting fungal community. We found nectar-consuming yeasts from Aureobasidium and Vishniacozyma genera and functionally diverse filamentous fungi from the Cladosporium genus dominated the anthosphere. The candidate core microbiota persisted across this dynamic niche despite high microbial turnover, as observed in shifts in community composition and diversity as flowers matured and senesced. The results demonstrated that floral stages are strong drivers of anthosphere fungal community assembly and dynamics. This study represents the first detailed exploration of fungi through floral development, building on fundamental knowledge in microbial ecology of healthy flowers.Item Open Access Endophytic fungal isolates from apple tissue: Latent pathogens lurking within?(Elsevier Ltd, 2024-06) Nwe, LL; Casonato, Seona; Jones, ElizabethFungal endophytes inhabit a similar ecological niche to that occupied by many phytopathogens, with several pathogens isolated from healthy tissues in their latent phase. This study aimed to evaluate the pathogenicity, the colonisation ability, and the enzyme activity of 37 endophytic fungal isolates recovered from apparently healthy apple shoot and leaf tissues. The pathogenicity of the isolates was assessed on ‘Royal Gala’ and ‘Braeburn’ fruit and detached ‘Royal Gala’ shoots. For the non-pathogenic isolates, their ability to endophytically colonise detached ‘Royal Gala’ shoots was evaluated. Enzyme activity assays were undertaken to determine whether the pathogenicity of the endophytes was related to the production of the extracellular enzymes, amylase, cellulase, pectinase, protease, and xylanase. Of the 37 isolates studied, eight isolates, representing the genera Colletotrichum, Diaporthe, Fusarium, and Penicillium, were shown to be pathogenic on both apple shoots and fruit. Two isolates identified as Trichoderma atroviride, were pathogenic only on shoots, and three isolates, representing the genus Diaporthe, were pathogenic only on fruit. Of the remaining 24 isolates, 22 (Biscogniauxia (n = 8), Chaetomium (n = 4), Trichoderma (n = 3), Epicoccum (n = 2), Neosetophoma (n = 2), Xylaria (n = 1), Daldinia (n = 1), and Paraphaeosphaeria (n = 1)) were recovered from the inoculated apple shoots but two failed to colonise the shoot tissues. Of the isolates tested, 20 produced amylase, 15 cellulase, 25 pectinase, 26 protease, and 13 xylanase. There was no correlation between the range and type of enzymes produced by the isolates and their pathogenicity or ability to endophytically colonise the shoot tissue. The study showed that approximately one-third (13/37) of the isolates recovered from the apparently healthy apple shoot tissues were observed as latent pathogens. The isolates that did not cause disease symptoms may have the ability to reduce colonisation of apple tissues by pathogens including Neonectria ditissima associated with European canker of apple.Item Open Access Improvement in microbiota recovery using Cas-9 digestion of Mānuka plastid and mitochondrial DNA(Springer Nature, 2024-12) Larrouy, Justine L; Ridgway, Hayley J; Dhami, Manpreet K; Jones, ElizabethUnderstanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.Item Open Access Prevalence and abundance of plant-parasitic nematodes in New Zealand maize fields: Effects of territory, soil orders, crop stage, and sampling time(Taylor & Francis Group, 2024) Nagarathnam, Thiruchchelvan; Kularathna, Manjula; Moukarzel, Romy; Casonato, Seona; Condron, LeoPlant-parasitic nematodes (PPNs) are significant agricultural pests that can reduce maize yields. This study examines the prevalence, abundance, and diversity of PPNs in New Zealand maize fields, focusing on the effects of territory, soil orders, crop stages, and sampling times. Seven PPN genera were identified: Pratylenchus spp. (root-lesion), Helicotylenchus spp. (spiral), Meloidogyne spp. (root-knot), Heterodera spp. (cyst), Paratylenchus spp. (pin), Criconemella spp. (ring), and Tylenchus spp. PPNs were present in 98% of the samples, with Pratylenchus spp. being the most prevalent (91%), followed by Helicotylenchus spp. (38%). Compared to Waikato and Manawatu-Whanganui, Canterbury had the highest nematode populations, particularly of Pratylenchus spp. and Helicotylenchus spp. Brown and pallic soils supported higher PPN abundances. Sampling during the maize harvesting stage and late autumn resulted in the highest nematode populations and diversity indices. Pratylenchus spp. populations often exceeded the economic threshold of 500 Pratylenchus kg‾¹ of soil, suggesting a significant threat to maize yield in New Zealand. The findings highlight the need for further research to assess the impact of Pratylenchus spp. on maize yield and to develop effective management practices for maize cultivation in the country.Item Open Access Diversity of mammalian species in the Kangchenjunga Landscape of eastern Nepal(Springer Nature, 2024-12) Lama, Sonam T; Bugler, Kathryn A; Ross, James; Paterson, AdrianThe Himalayas, including Nepal, are a biodiversity hotspot. However, records on mammalian richness remain incomplete due to resource limitations, inadequate training, and the remote location of study areas. The unprotected forest area of the Panchthar-Ilam-Taplejung region in eastern Nepal is a vital corridor connecting India and Nepal. Using a structured methodology we aimed to increase our knowledge of mammalian diversity in this area. Camera traps were deployed throughout the Panchthar-Ilam-Taplejung area in 53 locations in winter and 54 in spring, accumulating 3014 camera trap days and generating 93,336 images, with a positive trigger rate of 29.8%. The survey revealed 17 species of medium to large-sized mammals and an additional six species of smaller unidentified mammals, including two melanic variations and two previously undocumented species. Activity patterns were calculated for species with more than five image records in both seasons. The findings contribute essential information about the Kangchenjunga Landscape, which can be used to further conservation efforts in this critical ecosystem corridor.Item Open Access Why is single-use plastic still in the conservation sector toolbox?(Taylor & Francis, 2024-10-23) Pitt, Katie; Ross, James; Paterson, AdrianMicroplastic residue left in the environment from plastic chewcards in three pest mammal monitoring operations was estimated at an average of 15% of the starting weight. This finding highlight the issue of single-use plastics within New Zealand’s (NZ) conservation sector. A review of other research operations across NZ shows a significant number of plastic chewcards are deployed, potentially contributing to microplastic pollution in environmentally sensitive areas. Our research shows the need for sustainable alternatives to plastic chewcards in order to mitigate the environmental impact. Alongside an estimation of microplastic being left in the environment, we evaluated wood-pulp chewcards as a potential alternative to corflute chewcards, with results indicating wood-pulp cards maintain comparable interaction rates across key pest species. By identifying the environmental issues of microplastics in the environment and offering a potential alternative, we aim to open a dialogue about adopting more sustainable tools and practices in the NZ conservation sector.Item Open Access Prevalence and abundance of plant-parasitic nematodes associated with corn (Zea mays L.) in Anuradhapura, Sri Lanka(National Science Foundation of Sri Lanka, 2024) Thiruchchelvan, Nagarathnam; Casonato, Seona; Gunasingham, Mikunthan; Condron, Leo M; Moukarzel, Romy; Kularathna, ManjulaThe prevalence and abundance of plant-parasitic nematodes (PPNs) associated with corn (Zea mays; Poaceae) in the Anuradhapura district of Sri Lanka are poorly understood. This study investigated the occurrence and population densities of major PPN genera associated with corn. Over 92% of the corn fields were positive for PPNs in all the sampled fields. Major PPN genera identified were Pratylenchus spp. (71.4%), Helicotylenchus spp. (28.6%), Meloidogyne spp. (21.4%), Criconemella spp. (21.4%), and Hoplolaimus spp. (35.7%). The mean population density of Pratylenchus spp. was 2020 nematodes kg‾¹ of soil, in the Anuradhapura corn fields. During the cropping season from November (2021) to February (2022), all PPN genera except Meloidogyne spp. were observed. Pratylenchus spp. were detected at levels below 1000 nematodes kg‾¹ of soil at the seedling stage, except in Kelenikawewa where the initial population was 1865 nematodes kg‾¹. At the time of harvest, Pratylenchus spp. increased by 2 to 10 folds. These findings suggest a potential impact of Pratylenchus spp. on corn yield in Anuradhapura, highlighting the need for further research to assess damage levels and the overall effect of PPNs on corn production in Sri Lanka.Publication Open Access Evaluation of food grade products for attractancy to potato tomato psyllid adults infected with or without Candidatus Liberibacter solanacearum : A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Agricultural Science at Lincoln University(Lincoln University, 2024) Braidwood, Kate AliceTomato potato psyllid (Bactericera cockerelli (Šulc) (Hemiptera: Triozidae)) (TPP) is an insect, introduced to New Zealand in 2006, which causes significant damage to potato crops on the Canterbury plains of New Zealand. In this study three key aspects of integrated pest management, namely: trapping, biological control and identification of food grade attractants for utilization in a lure, were investigated. In addition, DNA integrity of TPP extracted off yellow sticky cards placed in vivo in potato paddocks was examined. A novel study of 75 food grade products were evaluated for attractancy to TPP adults. Choice testing using a Y-tube olfactometer found that a total of 16 products had attraction at ≥50% for “cold” TPP (i.e. insects with no infection of Candidatus Liberibacter solanacearum (CaLso)). Those attractants included: fatty acids (palm oil + lecithin granules; and macadamia nut oil + lecithin granules); glycerin flakes + lecithin granules; polysaccharides (xanthan gum, micro agar and iota carrageenan, primellose, fermented gelatin type B); disaccharide (trehalose) monosaccharide (xylose); amino acids (glutamine, methionine and valine) an alcohol (96% ethanol) and an acid (phosphoric acid). All of these products were subsequently evaluated for attractancy to “hot” TPP adults (i.e. insects confirmed positive by polymerase chain reaction (PCR) to CaLso). All the amino acids were marginally more attractive to “hot” TPP adults than “cold” ones: methionine (70% vs. 55% respectively), valine (65% vs 60%) and glutamine (55% vs. 50%). Similarly, primellose was also more attractive (60% vs 50% respectively). Xanthan gum, micro agar, trehalose and glycerin flakes + lecithin remained attractive (at 50%), whereas 96% ethanol (45%), iota carrageenan (40%), macadamia nut oil + lecithin granules (40%), phosphoric acid (35%), and palm oil + lecithin granules (25%) were all significantly less attractive than to cold TPP (P<0.01). Two insect traps were compared throughout the 2022/2023 season, the commonly used yellow sticky card and a novel 3-D printed yellow cup-trap, which was also designed to enable housing of an attractant lure. At low population numbers of TPP seen on the Canterbury plains (mostly only 1 or 0 per trap during 2022/23 potato growing season), both trap types were only partially successful in catching TPP. The highest number of TPP caught in late February/early March 2023 was 8 on a sticky card and 3 in a cup-trap. Inclusion of valine, trehalose and palm oil alone or in combination with each other in late summer did not improve efficiency of the cup-traps. To determine DNA integrity of TPP, an in vitro study of insects harvested from colonies raised in an acrylic sheet-covered greenhouse found that DNA of a single insect, captured off potato plant into a plastic vial, regardless of age, could be successfully amplified using PCR. In vivo studies found that at least 3 young, light-coloured, TPP adults must be combined in a pooled sample to successfully amplify their DNA. Pooled samples of 5 young TPP adults were placed on yellow sticky cards in vivo in a paddock in autumn. DNA of each pooled sample was then analysed using PCR on days 1 to 7, 10 and 14 in the field. DNA integrity was maintained up to 6 days under field conditions. This research successfully identified 13 potential products which show potential for use as an attractant lure, although performance in the field against low density populations was not strong. Field use of cone-shaped traps was the first in New Zealand, allowing the inclusion of a lure. In addition, TPP DNA extracted off yellow sticky cards over 1-14 days in the field, found reducing ability to detect TPP over time using PCR, leading to the recommendation that extraction was best done within 7 days, ideally 5 or more TPP as a pooled sample should be used for PCR extractions.Item Open Access Bridging aquatic invasive species threats across multiple sectors through One Biosecurity(Oxford University Press on behalf of American Institute of Biological Sciences, 2024-07) Bray, JP; Hewitt, Chad; Hulme, PhilipUnderstanding the magnitude of biosecurity risks in aquatic environments is increasingly complex and urgent because increasing volumes of international shipping, rising demand for aquaculture products, and growth in the global aquarium trade, are accelerating invasive alien species spread worldwide. These threats are especially pressing amid climate and biodiversity crises. However, global and national biosecurity systems are poorly prepared to respond because of fragmented research and policy environments, that often fail to account for risks across sectors or across stakeholder needs and fail to recognize similarities in the processes underpinning biological invasions. In the present article, we illustrate the complex network of links between biosecurity threats across human, animal, plant, and environment sectors and propose a universal approach to risk assessment. One Biosecurity is a holistic, interdisciplinary approach that minimizes biosecurity risks across human, animal, plant, algal, and ecosystem health and is critical to reduce redundancy and increase cross-sectoral cohesion to improve policy, management, and research in aquatic biosecurity.Item Open Access Preliminary survey of plant-parasitic nematodes associated with grapevines in Blenheim, New Zealand(New Zealand Plant Protection Society (Inc.), 2024-09-20) Moukarzel, Romy; Jones, Elizabeth; Ridgway, Hayley; Kularathna, ManjulaPlant-parasitic nematodes threaten horticultural crops, causing damage by feeding on plant roots, reducing yields, and affecting global food security. We present preliminary results on nematode genera found in soil around two varieties of grapevine (Sauvignon blanc and Pinot noir) with different rootstocks (101-14, SO4, 5C, Riparia Gloire, 3309, Schwarzmann) in ten vineyards located in Blenheim, part of the largest grape-growing area in New Zealand. Soil samples were collected, and nematodes were extracted using a modified centrifugal-flotation technique. Nematode counting and morphological identification to genus level was conducted based on characteristics such as stylet size and overall body shape. Soil texture analysis was performed, and the influences of grape variety and rootstock as well as soil type on nematode diversity were assessed. Four genera of plant-parasitic nematodes, including Pratylenchus, Paratylenchus, Helicotylenchus, and Criconomella, were recovered from the vineyard soils and a snapshot of relative abundance was determined. Differences in the nematode genera and their relative abundance among varieties and rootstocks were found, which suggests potential interactions between nematode genera and grapevine rootstocks/scions. This preliminary survey provides updated information on nematodes since the last survey conducted 20 years ago in New Zealand. This work indicates the presence of various genera of plant-parasitic nematodes in soils around grapevines grown around Blenheim, New Zealand. These findings highlight the need for further research to understand the interactions between nematodes, grape varieties, and rootstocks. The importance of addressing this knowledge gap for biosecurity measures and potential implications on grapevine growth and vineyard productivity is discussed.Publication Embargo Identification and characterisation of Phytophthora spp. in New Zealand apple orchards : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Toalak, MerriamApples, a prominent and widely favoured fruit crop on a global scale, are traded internationally and carry substantial economic importance worldwide. They play a vital role in New Zealand’s agriculture sector, with the World Apple Review consistently ranking the New Zealand apple industry as the most competitive in the world. Apple production encounters various challenges notably the adverse effects of pests and diseases, with Phytophthora crown and root rot being an important soil borne disease in all apple growing regions. Worldwide the disease is primarily caused by Phytophthora cactorum, although other species of Phytophthora have also been associated with crown rot of apple. The aim of this study was to determine the identity of Phytophthora species associated with apple orchards in New Zealand and explore their genetic structure and relative pathogenicity. Furthermore, the impact of two commercial microbial inoculants, arbuscular mycorrhizal fungi and Trichoderma species on the susceptibility of two apple rootstocks to P. cactorum infection in a whole-plant pathogenicity assay was evaluated. In Chapter 2 a survey was conducted to determine the Phytophthora species in the soils of apple orchards. The survey sampled soils from 12 different apple orchards of the five main apple growing regions in New Zealand: Hawke’s Bay (5 orchards), Tasman (4 orchards), Waikato (1 orchard), Otago (1 orchard) and Canterbury (1 orchard). Soil samples were obtained from blocks of the main orchard sites, with apple trees representing different cultivars and ages groups (young, medium and mature). The sampling included 11 orchard blocks from Hawke’s Bay, 13 in Tasman and 2 each from Otago, Waikato and Canterbury, resulting in a total of 30 blocks. The Phytophthora species were recovered by baiting using healthy Himalayan cedar needles (Cedrus deodara), lupin radicles (Lupinus polyphyllus) and apple cotyledons as baits. Lupin was the most effective bait, recovering 147 Phytophthora spp. isolates compared to apple cotyledon and cedar needle recovering 72 and 52 Phytophthora spp. isolates, respectively from the Hawke’s Bay, Tasman, Otago and Waikato samples (Canterbury samples baited with pine and rose). The 280 Phytophthora isolates recovered were identified based on combined results of morphology and DNA sequencing, with a total of seven species identified. These were Phytophthora cactorum, P. cambivora, P. megasperma, P. plurivora, P. rosacearum, P. chlamydospora, P. cryptogea and isolates with unresolved identity (Phytophthora spp.). The most prevalent species was P. cactorum. In Chapter 3, the genetic diversity within the P. cactorum population was determined using random amplified microsatellites (RAMS) and universally primed polymerase chain reaction (UP-PCR) primers and relative aggressiveness of the recovered Phytophthora species assessed using detached tissue assays. The 59 P. cactorum isolates were placed into five major groups of 3, 16, 9, 9 and 20 isolates each with two isolates each placed in groups by themselves, with the P. cactorum population in the orchards dispersed in the different groups. From the genetic diversity analysis isolates of P. cactorum and representative isolates of the different species recovered were selected and their aggressiveness assessed used a developed detached root assay and an existing shoot assay. All Phytophthora species and P. cactorum isolates tested were virulent on the apple rootstocks tested, with rootstock MM106 being more susceptible than M9 and M26. There was no correlation between the genetic diversity and aggressiveness. In Chapter 4 the pathogenicity of four P. cactorum isolates on whole apple plants was determined on MM106, M26 and M9 rootstocks. The rootstocks were inoculated by dipping in 1 × 105zoospores per mL or using 50 g colonized oats grain into the planting hole. All four P. cactorum isolates caused disease on all three apple rootstocks, with there being no difference in the disease score between rootstocks or isolates irrespective of the type of propagule used. In Chapter 5 the effect of inoculation with AMF and/or Trichoderma on susceptibility to P. cactorum infection and overall growth of young rootstock plants was investigated. Rootstocks M9 and MM106 were inoculated with AMF, Trichoderma and combined AMF and Trichoderma, and, after 60 days growth, inoculated with P. cactorum. At harvest, the AMF and/or Trichoderma inocula had no effect on P. cactorum disease level on either rootstock. However, in the absence of P. cactorum, inoculation with both Trichoderma and AMF tended to enhance growth compared to the control. Overall, this study has identified the Phytophthora diversity in New Zealand apple orchards and confirmed the pathogenicity of the recovered species, with particular emphasis on the dominant species, P. cactorum. The findings highlight that further studies are warranted including investigation of management strategies to reduce the potential threats posed by these pathogens.Item Open Access Genetic characterization and prevalence of Pseudomonas syringae strains from sweet cherry orchards in New Zealand(Wiley on behalf of British Society for Plant Pathology, 2023-12) Marroni, MV; Casonato, Seona; Visnovsky, SB; Pitman, AR; Beresford, RM; Jones, ElizabethBacterial canker of cherry, caused by Pseudomonas syringae pathovars, is a major constraint to cherry growing in New Zealand. The prevalence of strains from cherry orchards in Central Otago, the main growing area for cherries in New Zealand, was studied, to better understand the epidemiology of the disease. Pseudomonas spp. isolates were collected from symptomatic and asymptomatic cherry tissue from 23 commercial cherry orchards in 2015. Isolates were classified into strains belonging to three different taxonomic groups by determining their phylogeny using the gltA gene sequence for all the strains and multilocus sequence analysis (MLSA) of four housekeeping genes for 35 strains. Pathogenicity of all Central Otago strains was tested on immature cherry fruit to support the phylogenetic classification. The two main taxonomic groups were P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1), in Phylogroup 2 (PG2) and Phylogroup 3 (PG3), respectively. The third group comprised nonpathogenic strains classified as Pseudomonas spp. Strains of Psm1 formed a monophyletic group, representing an almost clonal population. There was more variation detected within strains of Pss, although they were restricted to group PG2d. Nonpathogenic Pseudomonas spp. and pathogenic Pss and Psm1 strains coexisted in the same orchard. It was concluded that Pss is the predominant pathovar in Central Otago. This is the first detailed study of the P. syringae species complex in cherry orchards in New Zealand and provides the basis for future epidemiology studies.Item Open Access Review of Pseudomonas species causing bacterial canker of Prunus species with emphasis on sweet cherry (Prunus avium) in New Zealand(Springer Nature, 2024-02) Marroni, MV; Casonato, Seona; Pitman, AR; Visnovsky, SB; Beresford, RM; Jones, ElizabethBacterial canker of cherry is a major constraint to stone fruit production worldwide, including New Zealand. Six pathovars of the bacterium Pseudomonas syringae are known to cause bacterial canker on Prunus species. From those six pathovars, P. s. pv. syringae (Pss), P. s. pv. morsprunorum race 1 (Psm1) and P. s. pv. persicae have been reported as pathogens of Prunus species in New Zealand, and Pss and Psm1 on sweet cherry (Pr. avium). On sweet cherry, extensive development of cankers and gummosis is usually observed, particularly during late winter and spring, with the progressive decline of trees resulting from the death of branches or death of the plant. In young orchards in New Zealand, losses of 20–50%, and sometimes the removal of entire cherry blocks have been observed. This review reports on the current knowledge of P. syringae pathovars causing bacterial canker of Prunus species, with specific focus on sweet cherry in New Zealand, and covers their identification, the infection process, virulence associated factors, epidemiology, symptoms, and management strategies.Item Open Access Genetic diversity and virulence variability in Diplodia mutila isolates from symptomatic grapevines in New Zealand: Virulence and genetic diversity of Diplodia mutila(Julius Kühn-Institute (JKI), 2023-04-23) Baskarathevan, J; Jones, Elizabeth; Jaspers, M; Ridgway, HGenetic diversity and virulence variability of Diplodia mutila isolates recovered from grapevines in New Zealand were investigated. The universally primed PCR (UP‐PCR) and vegetative compatibility group (VCG) methods were used to investigate the genetic diversity. Pathogenicity tests with ‘Sauvignon Blanc’ detached shoots and potted vines were used to determine the virulence diversity. UP‐PCR analysis determined eight genetic groups of D. mutila with 70% of the population within one group. Phylogenetic analysis also determined that New Zealand isolates were more closely related to Australian isolates than Californian isolates. Vegetative compatibility grouping analysis placed the isolates into three VCG groups with 57% of isolates belonging to all three VCGs. Vegetative compatibility reactions were observed among isolates, but this was not correlated with the genetic clustering. Virulence assays proved that all isolates tested were pathogenic on grapevine stems. Differences in necrotic lesions lengths caused by D. mutila isolates were identified, indicating different virulence levels among isolates, however, no relationship was found between the genetic groups and the virulence. The results of the study indicated movement of D. mutila isolates between nurseries, vineyards, and other sources in New Zealand. This information will inform control strategies to limit the further spread of this pathogen into vineyards in the same region or new regions.Item Open Access Predator-Free New Zealand 2050: Techniques for improving ground based control and monitoring of the brushtail possum(University of California, 2024-08-30) Ross, James; Graham, B; Pitt, K; Timm, RM; Woods, DMThe brushtail possum, a marsupial native to Australia, was widely introduced in New Zealand (NZ) to develop a fur industry. Before the settlement of humans in NZ, there were no terrestrial mammals; therefore, the local species evolved without mammalian predators. This resulted in native species populations declining at alarming rates and many possibly facing extinction on the NZ mainland, especially large-bodied endemic birds. In response to this problem, private investors (supported by the NZ government) developed an initiative to eradicate key mammal predators (possums, rats, and stoats) on the NZ mainland by 2050 (PFNZ2050). As a result, control efforts have significantly expanded over the past decade, and there are now 17 PFNZ2050 landscape projects covering 757,000 ha. Research has looked at combining audio, visual and social lures to improve control efforts for possums. Early results indicate that a combination of lures increases both encounter and interaction rates around control devices. In particular, the combination of audio and visual lures was consistently the top performer in both captive and small-scale field trials. Large-scale field trials are currently underway to confirm these initial results, investigating the effectiveness of combination lures paired with multi-kill AT220 possum traps. Additionally, the lures are being assessed at different times of the year and with varying possum densities. With the drive to PFNZ2050, pest mammal monitoring has markedly competing management control strategies. Traditionally, this has relied on single-use plastic monitoring devices such as chewcards and tracking tunnels. An investigation of pest-animal interaction with chewcards indicates that approximately 12% of plastic deployed ends up as microplastic pollution. Another NZ government initiative seeks to ban all single-use plastics, and research is currently investigating the efficacy of non-plastic (biodegradable) alternatives. This research also includes a cost-effectiveness analysis and the reliability of identifying animal bite marks on both plastic and non-plastic chewcards.