Treena Burgess

Estimates of invasion risk can support prioritisation of future threats from non-native species. Greater risk of invasion is expected when species occur in connected source regions and possess traits promoting successful transport, introduction or establishment. We compile a global database of first reports of Phytophthora de Bary species, a diverse oomycete genus attacking a broad range of plant hosts across multiple regions, sectors and ecosystem types with increasing frequency. Using Bayesian hierarchical zero-inflated models, we model global patterns of new detections since 2005 among 109 Phytophthora pathogens across 56 countries with at least two known Phytophthora species reported before 2005. We estimate the effects of trade connectivity, climate matching, national surveillance and pathogen traits on the probability of a new detection. We find that 69 (38%) Phytophthora species were either unknown or had no known source regions before 2005 and were therefore excluded from our analysis. Our study shows that invasion risk is increased for pathogens with broader thermal tolerance and the ability to produce survival structures linked to stress tolerance and asymptomatic infections. This knowledge can be used to enhance national horizon scanning and risk-based surveillance activities to better manage risks to plant health from emerging pathogens.

The variability of the rhizosphere microbial community has not been well-studied in avocado plantations at the field-scale. This research aimed to determine if the bacterial and fungal communities in the rhizosphere and/or the soil physicochemical properties from two commercial avocado orchards varied with different sampling designs (grid-based, longitudinal transect, and zigzag transect), and in turn if this changed the soil physicochemical properties driving the composition of the microbial communities. There were no differences in alpha diversity of bacteria or fungi based on sampling design in either orchard, and bacterial and fungal alpha diversity showed no evidence of spatial autocorrelation. Bacterial community composition in Orchard 1 varied with sampling design, whereas no differences were observed for bacterial community composition in Orchard 2 or for fungal community composition in either orchard. In each orchard, at least 50 % of the most abundant bacterial taxa were common between the sampling designs, however, less than 40 % the most abundant fungal taxa were common between the sampling designs. Canonical correspondence analysis indicated that the edaphic drivers of bacterial and fungal communities in Orchard 1 differed based on the sampling design. These results highlight the importance of field-scale sampling design for accurately characterising avocado rhizosphere bacterial and fungal communities particularly when such data will inform orchard management decisions. Soil sampling using a random, grid-based design is recommended as a simple and reliable method for monoculture fruit tree orchards.

Plant-soil feedbacks (PSFs) are essential for understanding plant community dynamics and ecosystem restoration. Glasshouse experiments provide controlled environments to study PSFs, but isolating biotic and abiotic influences remains challenging. Soil sterilization removes biotic components, with biotic effects restored via live inoculum. However, inconsistencies in sterilization methods, inoculum ratios, and storage practices complicate reproducibility. This literature review synthesizes 184 PSF studies from the past 24 years, to document methodological variation and reporting inconsistencies that influence experimental design, interpretation, and cross-study comparability, specifically highlighting variability in sterilization parameters and live inoculum application. Many studies overlooked nutrient flushes and persistent microbial activity post-sterilization. No consensus exists on live inoculum ratios, and storage practices remain poorly reported, limiting cross-study comparability. Reproducibility and realism in PSF estimates may be strengthened through measures including, but not limited to: (1) improved methodological reporting of core parameters, (2) validation of sterilization success, and (3) empirically determined inoculum ratios.

Tuber melanosporum was first harvested in Australia in 1999, and exports began in 2007. Australia is now the world's fourth-largest truffle producer. The main challenges Australian producers face are climate change, obtaining well-mycorrhized seedlings with no contaminants, and preventing entry of the contaminant species T. indicum and T. maculatum to Australia and T. brumale from east to Western Australia. There is also increasing competition from other southern hemisphere countries. Almost all truffle orchards in Australia are in regions with 600–1500 mm annual rainfall and a mean daily mid-summer temperature below 25 °C. As soils in agricultural lands of Australia are frequently acidic, lime is applied to achieve the alkaline pH required by truffles. New truffle orchards should be planned bearing in mind future climatic predictions. The incorporation of more T. borchii and T. aestivum in truffieres, and the possible use of T. magnatum will spread the harvest period, and thus exports. Oaks and hazel are currently used as major hosts, and new host species are being investigated, including Pinus. The cost of establishing a truffiere in Australia is high. However, Australia lacks many pests, diseases, and social problems associated with the European industry, and together with being an environmentally friendly industry, these factors make truffle production an attractive agricultural investment in Australia which will aid regional economies.

Truffles are possibly the only high-value cultivated organisms for which some aspects of the habit and life cycle have only recently been elucidated or remain unknown. Molecular techniques have helped explain the biological basis for some traditional empirical management techniques, such as inoculating soil with ascospores to improve yield, and have enhanced the detection of competitive or pathogenic soil microorganisms. Improved precision of assessment of the quality of inoculated seedlings is now possible. New knowledge of the genetic structure of populations has indicated that as trees age, the genotypes of mycorrhizae on inoculated trees change, and that there are large differences in the number of female and male genotypes participating in ascocarp formation. The plasticity of Tuber species has also been revealed, with maternal genotypes growing as an ectomycorrhiza in host tree roots and as surface mycelium or an endophyte in roots of adjacent non-mycorrhizal species. Refinement of management techniques has resulted from applying the new information, and the tools are now available to resolve the many outstanding gaps in our knowledge of Tuber biology.

Corymbia calophylla (marri), an iconic keystone species in the northern jarrah forest of southwestern Australia, is suffering from a stem canker disease caused by an endemic fungus, Quambalaria coyrecup . It is unusual for an endemic pathogen to have such a detrimental effect on a co‐evolved host, unless host defence mechanisms have been compromised. This study investigated the role of Phytophthora cinnamomi root infection and water shortage in predisposing C. calophylla to this canker disease, and whether these two stresses work synergistically to intensify the effect of the canker pathogen on C. calophylla . The roots of two‐year‐old C. calophylla plants were inoculated with P. cinnamomi in pot infestation trials, and 8 weeks later in the stems with the canker pathogen Q. coyrecup . Half of the plants were exposed to a water shortage treatment for the duration of the trial. Biophysical variables related to plant responses to the treatments were measured at harvesting. Reflectance spectroscopy measurements with a portable high‐resolution spectroradiometer were also taken weekly. The normalised difference spectral index (NDSI) was calculated for every combination of reflectance values between 350 nm and 2500 nm for all time points, correlated with treatment effects, and displayed as heat maps. Fifty‐seven vegetation indices (VIs), using wavelengths from different regions in the electromagnetic spectrum, were also calculated from the spectral data. Neither P. cinnamomi nor the water shortage treatments exacerbated the effect of the canker pathogen on the plants. The canker treatment increased plant stem diameter and canker volume significantly ( p < 0.001). The NDSI heat maps indicated that wavelengths in the electromagnetic spectrum's visible and shortwave infrared portions displayed the strongest correlations with the P. cinnamomi and water shortage treatments. For the canker treatment, it was the shortwave infrared portion. Six of the VIs responded significantly to the water shortage treatment: Carter index 1 ( p < 0.001), renormalised difference vegetation index ( p < 0.001), normalised difference water index ( p = 0.012), normalised phaeophytinization index ( p < 0.001), photochemical reflectance index ( p < 0.001) and red‐green ratio index ( p = 0.018). The renormalised difference vegetation index was also sensitive to the canker treatment ( p < 0.001), and the Carter index 1 to the P. cinnamomi treatment ( p < 0.001). Reflectance spectroscopy was able to track biochemical changes in C. calophylla leaves due to inoculation with P. cinnamomi , Q. coyrecup, and the water shortage treatment. However, more work must be done to identify optimum wavelengths specific to C. calophylla and its responses to pathogens.

The plant pathogen Phytophthora cinnamomi has significantly damaged the floristic diversity and community structure of the jarrah (Eucalyptus marginata) forest in Western Australia. Complete eradication of the pathogen from infested sites is not possible. This study assessed the feasibility of rehabilitating P. cinnamomi-infested forest sites with native resistant species using various methods of seed deployment. Precision burial of seeds at 5 mm was used as a control, mimicking optimum recruitment depths for many native species and compared against the use of extruded pellets (hereafter ‘pellets’) as an alternative method of precision seed placement. Eighteen rehabilitation plots were set up in three P. cinnamomi-infested reserves using six species. For Acacia acuminata, A. saligna, Calothamnus sanguineus and Melaleuca seriata, there were three treatments: precision buried (non-pelleted) seeds, pellets and pellets with an additive (i.e., a rhizobium bacterium for the Acacia spp. and ectomycorrhizal fungus spores for C. sanguineus and M. seriata). Banksia sessilis and Hakea laurina had only two treatments: precision buried (non-pelleted) seeds and pellets. Seedlings of all six species emerged successfully in P. cinnamomi-infested sites, and the numbers ranged between 23% and 88%. The survival of emerged seedlings after 9 months ranged between 16% and 84%, except M. seriata, which emerged at 59% but failed to survive. In most species, except A. acuminata, seedling emergence and survival from pellets were similar and within an acceptable seedling establishment range when compared to non-pelleted seeds. Pelletised seed with the addition of beneficial microbes did not improve seedling survival or shoot growth in the diseased areas of the jarrah forest. Overall, the results suggest that seedlings of resistant native species can successfully establish in P. cinnamomi-infested sites and pelletised seeds can be used as a viable method for precision planting.

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research.

The genus Phytophthora contains many destructive and globally important plant pathogens. In the last decade, targeted sampling efforts have resulted in a dramatic increase in the number of known species, as well as a better understanding of their global distribution. Routine activities undertaken in botanical gardens, combined with great numbers of local and international visitors, place botanical gardens at risk to the accidental introduction and establishment of pathogens such as Phytophthora spp. In this study, the occurrence of Phytophthora was investigated in two botanical gardens in the KwaZuluNatal Province of South Africa. Symptomatic collar and stem tissues were collected, and root and rhizosphere soil samples were taken from trees exhibiting symptoms of decline. Standard baiting techniques and direct plating of symptomatic tissues revealed the presence of seven species of Phytophthora residing in four phylogenetic clades. Five of these species, P. cinnamomi, P. citrophthora, P. multivora, P. parvispora and the informally designated taxon Phytophthora sp. stellaris were known to be present in South Africa and P. aquimorbida was recorded for the first time. Of these, P. citrophthora represented a novel host-pathogen association causing bleeding cankers on indigenous Celtis africana. A multilocus phylogenetic analysis based on ITS, βtub, cox1 and hsp90 sequences showed the presence of an undescribed species belonging to the Phytophthora ITS Clade 5. This species is described here as Phytophthora mammiformis sp. nov. This study highlights the importance of monitoring botanical gardens for the detection and discovery of pathogens and emphasises their value as sites for the discovery of novel host-pathogen associations.

The oomycete genus Phytophthora includes plant pathogens that pose significant threats to agricultural systems, natural ecosystems and urban forests. Urban forests are increasingly recognized for their role in mitigating climate change impacts and urban greening initiatives are underway worldwide. However, research suggests that the urban forest is also a reservoir of Phytophthora diversity, acting as bridgeheads for the introduction of these pathogens into production and natural ecosystems. The source of Phytophthora in urban forests is linked to anthropogenic factors, with the live plant trade the primary pathway. This study focused on the incidence and diversity of Phytophthora in amenity tree nursery stock in eastern Australia, primarily New South Wales, with one nursery from Victoria. The findings revealed a high incidence of Phytophthora in nursery stock destined for urban greening projects, having an overall positive rate of 22.1%, with incidence in individual nurseries ranging from 2.5% to 32%. The study detected 13 described Phytophthora species that are considered polyphagous on woody hosts and three lineages that potentially represent novel species. In addition, the detection of P. mediterranea and P. heterospora represent first reports for Australia, with P. mediterranea considered a biosecurity concern. The study highlights the substantial risk associated with the live plant trade as a source of Phytophthora introduction into urban forests and beyond. These findings underscore the urgent need to strictly implement clean nursery management practices to reduce the economic and environmental risks associated with Phytophthora in urban greening programmes.