Giles Hardy

Phytophthora is a long-established, well-known, and globally important genus of plant pathogens. Phylogenetic evidence has shown that the biologically distinct, obligate biotrophic downy mildews evolved from Phytophthora at least twice. Because, cladistically, this renders Phytophthora “paraphyletic,” it has been proposed that Phytophthora evolutionary clades be split into multiple genera (Crous et al. 2021; Runge et al. 2011; Thines 2023, 2024). In this letter, we review arguments for the retention of the generic name Phytophthora with a broad circumscription made by Brasier et al. (2022) and by many delegates at an open workshop organized by The American Phytopathological Society. We present our well-considered responses to the genus splitting proposals, both in general terms and in terms of the specific proposals for new genera, alongside new information regarding the biological properties and mode of origin of the Phytophthora clades. We consider that the proposals are mostly non-rigorous and not supported by the scientific evidence. Further, given (i) the apparent lack of any distinguishing biological characteristics (synapomorphies) between the Phytophthora clades; (ii) the fundamental monophyly of Phytophthora in the original Haeckelian sense (Haeckel 1877); (iii) the fact that paraphyly is not a justification for taxonomic splitting; and (iv) the considerable likely damage to effective scientific communication and disease management from an unnecessary breakup of the genus, we report that workshop delegates voted unanimously in favor of preserving the current generic concept and for seeking endorsement of this view by a working group of the International Commission on the Taxonomy of Fungi.

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.

Cold plasma is a promising non-thermal method for managing postharvest pathogens that cause mould and fruit decay. This study evaluated cold plasma (CP) and plasma-activated water (PAW) to control the postharvest fungal pathogens associated with strawberries. Fresh ‘Fronteras’ strawberries were treated with CP, PAW, or PAW applied as a mist (PAWM), and quality parameters, including spoilage, firmness, colour, and weight were measured on days 0 and 6. Propidium monoazide (PMA), a dye that selectively binds to the DNA of non-viable cells and prevents PCR amplification, was used to differentiate between viable and non-viable fungi following treatment. Strawberries treated with CP or immersed in PAW for 60 s had significantly reduced visible decay at day 6 without affecting fruit quality, but PAWM was ineffective at reducing spoilage. All treatments significantly reduced fungal diversity when measured using PMA-based metabarcoding after storing for 6 d at 4 °C, compared to the untreated control, with significantly lower abundance of viable fungi. Viable Cladosporium (strawberry pathogen) and Rhodotorula (biocontrol for berry fruit) accounted for 98 % of fungal communities in all treatments after 6 d. Differential abundance analysis showed that all treatments inhibited Filobasidium and Cystofilobasidium while reducing Botrytis abundance. These results demonstrate the potential of CP and PAW treatments to reduce fungal communities, including pathogens, and thus spoilage of postharvest strawberries.

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.

Native bee populations are generally in decline, and although their conservation needs are recognised, habitat requirements for the majority of species remain unknown. Many bee species construct nests underground, including the native Australian bee Lasioglossum (Homalictus) dotatum . However, like most ground‐nesting bees, their nesting ecology, particularly their substrate preferences and soil surface requirements, remains poorly understood. To address this knowledge gap, this study examined whether L. dotatum prefers nesting in bare sand or amid rock gravel and whether soil treatment influences nest‐site selection. Experiments were conducted using 24‐L pots of Bassendean sand, placed near active L. dotatum nesting aggregations. Ten pots had a layer of rock gravel, while the remaining 10 were left bare. Within each treatment, half of the pots contained untreated sand, and half contained steam‐treated sand to remove potential contaminants. This design tested whether L. dotatum prefers certain soil conditions and surface features when selecting nest sites. Results showed that female L. dotatum preferentially nest in pots with rock gravel over those with bare sand, suggesting that rock cover may create a more favourable environment by moderating temperature, retaining moisture, or providing structural stability for nest entrances. Additionally, females preferred steam‐treated sand over untreated sand, possibly indicating that factors associated with untreated soil, such as microbial presence or organic residues, may deter nesting. This study advances our understanding of L. dotatum nesting behaviour and provides a framework for creating pollinator‐friendly spaces by identifying key soil and surface features that influence nest‐site selection. However, the mechanisms driving their preference for steam‐treated sand remain unknown, highlighting the need for further research to distinguish the roles of hygiene, soil properties and potential chemical cues in nest‐site selection.

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 resilience of forests worldwide is challenged by climate change. Large-scale tree mortality and dieback events have been documented across continents in recent decades. The adaptive capacity of forests is important for predicting forest resistance and resilience to future climates yet remains largely unknown. We grew 12 populations of a widespread foundation tree species (Corymbia calophylla), originating from different temperature and rainfall regimes, in two common garden trials in Western Australia that had similar temperature but contrasting rainfall conditions. We quantified intraspecific trait variation at these two sites to estimate genetically determined trait variation with climate origin (genetic adaptation) and trait variation associated with environment (phenotypic plasticity). We aimed to determine the 1) contribution of genetic and environmental factors on growth, functional, and physiological trait variation; 2) coordination of leaf traits within the context of the leaf economic spectrum (LES) in variable rainfall conditions; and 3) role of local or regional climate adaptation influencing tree growth and water use efficiency. Growth and physiological traits were differentially expressed across populations and sites, highlighting the importance of genetic adaptation and phenotypic plasticity. Leaf traits reflected a more water conservative strategy with higher water use efficiency, high foliar nitrogen content, and low specific leaf area, as predicted by the LES, in trees at the dry site measured in autumn after the warm summer. Local adaptation was detected in growth and leaf water use efficiency traits at the regional climate, not the local population, scale. Plants from the cool region had greater performance than those from the warm region in most plant traits. Home-site rainfall was not a good predictor of trait expression. The capacity of C. calophylla to respond to low water availability through genetic adaptation and phenotypic plasticity may enable it to maintain optimal performance in drier conditions associated with climate change.

Spoilage of postharvest strawberries by fungal pathogens is a major global concern. This study employed culture-dependent and culture-independent methods to identify postharvest fungal communities of strawberries in Western Australia (WA). Ripe strawberries from eight varieties were sampled twice, early and late in the growing season, from 20 farms in two growing regions. At the first sampling time, traditional isolation and identification demonstrated a high abundance of Botrytis and Cladosporium in Region 1. Mucor was abundant at the second sampling time in Region 1 and both times in Region 2. Metabarcoding confirmed variety-specific fungal communities in WA strawberries. Botrytis and Cladosporium were predominant in Region 1 and Region 2 samples with more than 50% read abundance except on variety Suncoast. No Mucor sequences were detected using metabarcoding, although they were isolated from all samples using culture-based methods. Sisquoc, a hydroponic variety, had a significantly higher fungal diversity than the soil-grown varieties. Varieties Suncoast and Albion exhibited the lowest fungal diversity compared to others. This study demonstrated the value of using culture-dependent and culture-independent methods to investigate the complexity of fungal microbiomes of postharvest strawberries.

The high cost of native seeds and low seedling establishment percentages after seed broadcasting are major constraints for seed-based rehabilitation. This study examines whether extruded seed pelleting can be used as a tool to distribute seeds more effectively (e.g. distribute small seeds in a precise manner) while maintaining or enhancing seedling emergence and establishment of Australian shrub species used in the rehabilitation of Phytophthora cinnamomi infested Jarrah (Eucalyptus marginata) forest sites. Pellet formulation was first tested using five different formulations of dry ingredients and the addition of seeds from four Phytophthora-resistant species under glasshouse conditions. The best performing formulation from this work was then adopted to compare laboratory-produced and field-deployed pellets. Seedling emergence of the larger seeded species, Raspberry Jam Wattle (Acacia acuminata) and Pin-cushion Hakea (Hakea laurina), was highest using field-deployed pellets and emergence was statistically similar to the non-pelleted seeds. Seedling emergence reached 100% for the small seeded species, Silky-leaved Bold Flower (Calothamnus sanguineus) and Melaleuca seriata, from laboratory-produced pellets and was significantly higher than non-pelleted seeds. These results indicate that extruded pelleting offers an alternative direct seeding option that can result in greater or equal seedling emergence than that observed with non-pelleted seeds, yet the responses are species-specific. These species-specific pelleting techniques must now be tested under field conditions to confirm whether pellet production method and delivery improve seedling establishment under field conditions.