ItemImplementing biosecurity in live plant trade networks : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2022) Marshall, MadelineNew Zealand faces unique challenges with regards to invasive species due to a high number of endemic species and correspondingly high risk for the decline of indigenous species as a result of invasive introductions. Many of these introductions have been facilitated by human mediated transport, which promotes long range movement of plants and associated pests and pathogens. The transportation of these invasive species to new environments can negatively affect native plants, crops, and industries reliant on plant production. In particular, live plant trade networks represent effective mediums to disseminate invasive species such as pathogens, pests, and weeds. The movement of live plants through professional nurseries and private retailers in New Zealand is yet to be fully investigated. Performing an assessment of contact structures derived from live plant trades can be used to prevent the introduction and spread of invasive species, thereby safeguarding both businesses and the environment. Network analysis provides suitable tools to study live plant trade systems, such as the bilateral plant nursery network, as well as the itinerary online sales network. Fundamental characteristics related to geographic distribution of plant sales (such as location of origin and destination) and key metrics related to plant product movement within live plant trade networks need to be examined in order to better understand the nature of this structure. This thesis addresses gaps in knowledge related to live plant trade in New Zealand by generating networks that characterise human-mediated movement of horticultural products. Subsequently, developing network models of such systems was used to determine their vulnerability to invasive species acquisition and spread. This was accomplished via the assessment of three live plant trade systems of particular relevance to New Zealand biosecurity. These studies thusly characterise the forestry nursery transport network, the initial incursion of the invasive plant pathogen myrtle rust (Austropuccinia psidii) into New Zealand, and plant sales facilitated by the New Zealand-based online retailer Trade Me. Firstly, assessment of the forestry nursery transport network described the movement of product from seed orchards to nurseries to plantation forests and the biosecurity protocols in place at forestry nurseries. This study identifies seed orchards as the point of production most likely to facilitate widespread dispersal of a pathogen through the industry. The second study system, assessment of the initial incursion of myrtle rust into New Zealand, characterises the sale of nursery plants from myrtle rust positive nurseries during the first three months of the incursion. These networks identified a lack of comprehensive record keeping at ornamental nurseries as a risk for future invasions that are facilitated by contaminated nursery stock. Additionally, assessment of all myrtle rust positive locations during the first two years of the incursion identified delimiting surveys as a highly successful surveillance tool that would benefit from more research into optimisation of the survey radius depending on the nature of the invasive. The third and final study system, which characterised plant sales facilitated by Trade Me, employed the networking of plant sales based on their subcategorisation on the Trade Me site (into one of nine subcategories chosen by Trade Me) as well as the suburb of residence for both the seller and buyer of a product. Additionally, an assessment of the most common taxa sold on the site was conducted. The information derived from this study can be adopted for immediate use in biosecurity responses in the event of an introduction of an unwanted pest or pathogen vectored on ornamental plants, as well as identify the plant product classes at highest risk for long-distance dispersal. ItemSeed treatment options for New Zealand carrot production : A thesis submitted in partial fulfilment of the requirements for the Degree of Master at Lincoln University(Lincoln University, 2023) Spencer, EdwinThe New Zealand carrot industry currently uses fungicide seed coatings, rather than using some of the biological options available for disease control. The industry standard seed treatment has been in use since at least 2008. This research had the aim of comparing the current seed treatment with a pre-commercial biological (Trichoderma) seed treatment under a variety of conditions to determine the best approach. Data were gathered to show the effects of the various seed treatments on the carrots’ emergence, harvest weights, disease severity, and storage ability. A total of four experiments were conducted, two in the field and two in the glasshouse. A further experiment assessed the effects of all the pesticides applied to the crop or seed on Trichoderma conidia germination. A field trial was established in a commercial crop at Waiuku with five different seed treatments, including the combination of chemical and biological seed treatments. Unfortunately, due to covid restrictions, no data could be gathered until final carrot harvest, and harvested carrots were used in a cool store based storage trial. The Trichoderma alone treatment significantly increased yield over the industry standard seed treatment but there was no difference in storage performance among the treatments. A second field trial at Lincoln compared between chemical and Trichoderma seed treatments and untreated seed. These carrots were grown at a site known to contain soil-borne pathogens, and the crop received no pesticide applications. The aim was to investigate whether Trichoderma could provide long term disease control and increase marketable carrot yield. The carrots were also ground stored for a month after harvest to further test any long term disease suppression. However no significant differences were recorded among the treatments for any of the parameters measured. The glasshouse trials used soil from major carrot growing areas of New Zealand and looked at how chemicals and Trichoderma could help reduce the impact of the pathogens present compared to untreated seed. Additional data related to growth promotion such as foliage, taproot, and fine root weight were also recorded. Both trials tended to show that both the Trichoderma and chemical seed treatment had comparable performance in emergence and disease control and that this exceeded that of untreated seed. No growth promotion effects were recorded based on the dry weights of the foliage, taproots, or fine roots. To test Trichoderma conidia germination in the presence of pesticides, conidia were incubated at 25°C in the presence of pesticides at label rate concentrations. Glyphosate, difenoconazole, and mancozeb completely inhibited conidia germination but the seed treatment fungicides did not. Overall the results suggest that, under the conditions used, a Trichoderma seed treatment had a similar performance to the commonly used fungicide seed treatment. There was no best seed treatment in this study, but more options have been identified. The results in glasshouse conditions were not replicated in the field. The results also suggest that this strain of Trichoderma did not provide long term disease control, or promote carrot growth. The compatibility results showed that these strains of Trichoderma are sensitive to some pesticides but they are pesticides that are unlikely to come into direct contact with the conidia. The seed treatment fungicides did not affect conidial germination. ItemPreadaptation, hybridisation, and breeding system shape the invasion of three Rumex species in New Zealand : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2022) Savinen, Sandra ElisabetResearch has previously shown that Rumex (Polygonaceae) species introduced to New Zealand have multiple potential drivers behind their success, such as phenotypic plasticity, enemy release, and niche shift. However, it is not known whether these changes were caused by post-introduction evolution, or what other drivers could explain the success of these agricultural weeds. I combined demo-genetic traits and processes to assess how hybridisation and introgression, genetic differentiation, and breeding system contribute to the invasiveness of three introduced Rumex species. I compared plants from the species’ native (Europe, mainly the UK) and introduced (New Zealand) range and assessed whether the success is more likely due to prior adaptation or post-introduction evolution. Ploidy is associated with increased invasiveness, and if a species has multiple geo-cytotypes, higher ploidies are often found within the introduced range. Similarly, self-compatibility can help introduced populations to counter mate limitation and mixed mating can introduce new alleles to populations. I found no differences in genome sizes or chromosome numbers between plants from the two ranges using flow cytometry and manual chromosome counts. In addition, a comparison between bagged and unbagged Rumex conglomeratus plants showed no consequences from selfing, indicating mixed mating strategies. Surprisingly, the overall seed viability was lower for provenances from the introduced range compared to the native range. Hybridisation and introgression can increase genetic variation and help with adaptation to new environments. In a field survey, hybrid plants were found in New Zealand. However, the majority were likely first-generation hybrids, making introgression an unlikely driver behind the invasiveness. In addition, the parent species co-occurrence was lower in New Zealand compared to the UK. Lastly, genetic differentiation can indicate the origin of the introduction, as well as how likely a post-introduction evolution is a driver behind the invasiveness. A minimal differentiation was revealed by genotyping-by-sequencing both within but also between the native and introduced ranges. The population genetic analyses suggest that the UK is a likely origin for these species but admixture from elsewhere was also found. This would have likely helped the introduced populations to maintain comparable level of genetic variation to the native populations. As limited differences were found between the native and introduced populations, the investigated traits and processes are unlikely to explain the invasiveness in New Zealand. Rather, the success of these species is likely caused by prior adaptation. In addition, as these species are primarily agricultural weeds within both provenances, anthropogenically induced adaptation to invade is likely the main driver behind the success of these species. This method of adaptation, likely coupled with jack-of-all-trades genotypes, have allowed the species to thrive in manmade habitats, all around the globe. Thus, similar weeds within these habitats need to be carefully monitored to prevent further invasions in the future. ItemPurification of high-molecular-weight antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates(Multidisciplinary Digital Publishing Institute (MDPI), 2022-10) Babar, TK; Glare, Travis; Hampton, John; Hurst, MRH; Narciso, JO; Beattie, ABrevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium belonging to the Brevibacillus brevis phylogenetic cluster. Globally, insect pathogenic strains of the bacterium have been isolated, characterised, and some activities have been patented. Two isolates, Bl 1821L and Bl 1951, exhibiting pathogenicity against the diamondback moth and mosquitoes, are under development as a biopesticide in New Zealand. However, due to the suspected activity of putative antibacterial proteins (ABPs), the endemic isolates often grow erratically. Various purification methods, including size exclusion chromatography, sucrose density gradient centrifugation, polyethylene glycol precipitation, and ammonium sulphate precipitation employed in this study, enabled the isolation of two putative antibacterial proteins of ∼30 and ∼48 kD from Bl 1821L and one putative antibacterial protein of ∼30 kD from Bl 1951. Purification of the uninduced cultures of Bl 1821L and Bl 1951 also yielded protein bands of ∼30 and ∼48 kD on SDS-PAGE, which indicated their spontaneous induction. A disc diffusion assay was used to determine the antagonistic activities of the putative ABPs. Subsequent transmission electron microscope (TEM) examination of a purified putative antibacterial protein-containing solution showed the presence of encapsulin (∼30 kD) and polysheath (∼48 kD)-like structures. Although only the ∼30 kD protein was purified from Bl 1951, both structures were seen in this strain under TEM. Furthermore, while assessing the antibacterial activity of some fractions of Bl 1951 against Bl 1821L in the size exclusion chromatography method, the population of Bl 1821L persister cells was noted. Overall, this work added a wealth of knowledge about the purification of the high-molecular-weight (HMW) proteins (bacteriocins) of Gram-positive bacteria including Bl. ItemPurification of high molecular-weight antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates(MDPI, 2022-08-29) Babar, TK; Glare, Travis; Hampton, John; Hurst, MRH; Narciso, JO; Beattie, ABrevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium belonging to the Brevibacillus brevis phylogenetic cluster. Globally, insect pathogenic strains of the bacterium have been isolated, characterised, and some activities patented. Two isolates, Bl 1821L and Bl 1951, exhibiting pathogenicity against the diamondback moth and mosquitoes, are under development as a biopesticide in New Zealand. However, due to the suspected activity of putative antibacterial proteins (ABPs), the endemic isolates often grow erratically. Various purification methods including size exclusion chromatography, sucrose density gradient centrifugation, polyethylene glycol precipitation, and ammonium sulphate precipitation employed in this study enabled the isolation of two putative antibacterial proteins of ~30 kD and ~48 kD from Bl 1821L and one putative antibacterial protein of ~30 kD from Bl 1951. Purification of the uninduced cultures of Bl 1821L and Bl 1951 also yielded the protein bands of ~30 kD and ~48 kD on SDS-PAGE which indicated their spontaneous induction. Disc diffusion assay was used to determine the antagonistic activities of the putative ABPs. Subsequent transmission electron microscope (TEM) examination of purified putative antibacterial protein-containing solution showed the presence of encapsulin (~30 kD) and polysheath (~48 kD) like structures. Although only the ~30 kD protein was purified from Bl 1951, both structures were seen in this strain under TEM. Furthermore, while assessing the antibacterial activity of some fractions of Bl 1951 against Bl 1821L in size exclusion chromatography method, population of Bl 1821L persister cells was noted. Overall, this work added a wealth of knowledge for the purification of the HMW proteins (bacteriocins) of the Gram-positive bacteria including Bl.