The introduced plant pathogen Phytophthora cinnamomi Rands has caused extensive loss of understorey vegetation cover in native ecosystems globally. Vegetation loss likely has cascading impacts on fauna, but these are largely undocumented. One group of plants notably impacted by the pathogen are Xanthorrhoea grasstrees, which provide important habitat for digging mammals, so-called 'ecosystem engineers', such as bandicoots. We examined whether the quenda, Isoodon fusciventer, a bandicoot species endemic to southwestern Australia and an important ecosystem engineer, alters its foraging behaviour in forest infested by P. cinnamomi. We surveyed quenda digging activities in P. cinnamomi-infested and adjacent non-infested jarrah (Eucalyptus marginata) forest in peri-urban reserves and recorded the availability of plant cover and Xanthorrhoea preissii densities that could be used as refuge habitat, to determine if this was the case. We also recorded the availability of truffle-like fungi, an important food for quenda. Compared to non-infested forest, P. cinnamomi-infested sites had 46% less available quenda habitat in the form of dense, low shrubs. Downturned X. preissii 'skirts' of dead leaves touching the ground provide important quenda habitat. Infested sites had 45% fewer habitable (skirted) X. preissii. Infested sites also had 40% more bare ground. Quenda foraging activity was 33% lower within P. cinnamomi-infested sites and varied among reserves, suggesting the importance of site factors. We located few truffle-like fungi, with no significant difference between infested and non-infested forest, but we did not quantify all food sources used by these omnivores. We interpreted lower foraging in infestations as being due to reduced refuge habitat rather than reduced food availability. Our findings stress the importance of dense-skirted X. preissii and low-shrubs as quenda habitat. Management of pathogen spread is essential to retain quenda habitat. We invite further research into identifying pathogen-resistant shrubs and X. preissii to bolster quenda habitat in P. cinnamomi-infested forest.

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 degrees 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.

ABSTRACT 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.

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. Traditional and molecular approaches identified Botrytis and Cladosporium-dominated fungal communities in eight varieties of postharvest strawberries, collected from two different regions of Western Australia.image

Invasive plant pathogens cause considerable forest loss worldwide. However, little is known about how tree populations recover post-invasion. In Western Australia, Phytophthora cinnamomi 'dieback' affects jarrah (Eucalyptus marginata), with historical records of mass deaths in this keystone tree species due to infestation, resulting in permanent loss of standing forest. Historical observations of marri (Corymbia calophylla), a co-dominant keystone jarrah forest tree, suggest it is resistant to P. cinnamomi. Impacts of P. cinnamomi on the population dynamics of jarrah and marri are unknown. We recorded densities and stem diameters of jarrah and marri in a peri-urban forest to examine their population demographics in >60-year-old P. cinnamomi infestations compared with adjacent non-infested forest. While seedling (<0.5 cm stem diameter, similar to 2 -15 cm tall) densities were not significantly different, total tree densities were 43% (jarrah) and 48% (marri) lower for infested sites. Densities of jarrah 0.5-9 and 20-29 cm stem diameters were lower within infestations. Survival probabilities of jarrah seedlings were significantly greater in P. cinnamomi infestations, but those of mature jarrah were not different. While average marri stem density was 49% greater within infestations, densities of small marri (<20 cm stem diameter) were lower within infestations. Survival probabilities for marri seedlings were significantly decreased in infestations, while there was greater survival probability for mature marri within P. cinnamomi infestations. Our data suggest recruitment of jarrah and marri has likely reduced since P. cinnamomi invasion. This is the first documented impact on marri, which indicates that we have been overlooking the risk of decline due to P. cinnamomi for this species. We stress the need for continued management and highlight the necessity of planting seedlings similar to 6 months old, and assisting their survival with phosphite and fertilizers, to bolster local tree populations.

Damping-off oomycete and fungal plant pathogens reduce the germination, emergence, and survival of seedlings. In agricultural systems, this poses a significant problem as it may reduce productivity; in contrast, the impact is more subtle in natural ecosystems and may be essential for maintaining the structure and diversity of plant communities. The oomycete genus Phytophthora is frequently detected in natural plant communities causing disease in mature plants, but it is rarely assessed as a damping-off pathogen. A pathogenicity experiment was established with five oomycete treatments, three putatively native Phytophthora species, the invasive P. cinnamomi, and Pythium irregulare, to determine the damping-off host range in selected plant species from a hyper-diverse Mediterranean-type ecosystem. Additionally, plant and seed traits were analysed to determine if they were correlated with susceptibility to pre-emergent damping-off. Phytophthora arenaria was the only putatively native generalist damping-off pathogen, causing 12 of 19 plant species to experience significantly reduced seedling emergence or survival relative to the control treatment. Pythium irregulare and the introduced P. cinnamomi caused significant damping-off for 12 and 13 plant species, respectively. Plant species that were slowest to germinate and emerge were the most susceptible to pre-emergence damping-off caused by P. arenaria. These results suggest native and invasive Phytophthora may substantially influence the structure and diversity of natural plant communities through damping-off. While mature plant species are the most common focus in Phytophthora research, our study indicates damping-off should be considered to determine the full impact of these soil-borne plant pathogens.

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.

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.

Phytophthora root rot is a major problem for avocado growers around the world. This review summarises the current control measures and their impact on the soil microbiome. The fungicide phosphite is widely used in the avocado industry, and reports from several countries indicate that Phytophthora cinnamomi is developing resistance. For this reason, alternative control measures have been investigated. Applying organic mulches and soil dressings of calcium or silicon provides a level of control. Biological control through the application of suppressive microbes has been actively investigated over many years, but reports of successful field deployment are rare. This review examines the effects on the soil microbiome of these control measures and assesses the future directions for research.

This review assesses possible reasons for the discrepancy between the high numbers of Phytophthora species and putative new species isolated from environmental samples using metabarcoding, compared with the low number cultured and identified through bating. Molecular protocols are unlikely to result in high numbers of false positives, except that variants in young hybrid species may be incorrectly identified as different species. Baiting conditions favour parasitic species that are fast to sporulate, able to infect a range of bait species, achieve infection with a low number of zoospores, and fast-growing on selective agar. Species may not be isolated because they are slow-growing saprophytes and slow to sporulate when baited. Changes to protocols that might result in the isolation of more species include changes in the timing of exposure of baits, inclusions of dead baits, reducing potential competition from fast-growing species by baiting only small volumes of soil, and isolation on media without antimicrobials. However, the species not isolated may have growth traits precluding easy isolation, such as host specificity or obligate biotroph lifestyle.

For most Western Australian plant species, no information is available on the effect of Phytophthora cinnamomi on seedling emergence, early survival, and early plant growth. Such information is required when selecting species for rehabilitating Eucalyptus marginata (jarrah) forest areas affected by Phytophthora dieback. This study evaluates the response of several native species to P. cinnamomi to identify those resistant to the pathogen at the early stages of plant development. Firstly, the effect of P. cinnamomi on seedling emergence and early survival was evaluated for 50 native species. Then, 24 species were selected and tested for their resistance to P. cinnamomi when more mature. They were infested at 5–7 months old and disease impact assessed after two months. Of 38 species that emerged in sufficient numbers for statistical analysis, P. cinnamomi did not affect either emergence or survival of 9 species, emergence or survival was decreased in 14 species, and both emergence and survival were significantly decreased in 15 species. Of the species tested at 5–7 months old, two were resistant, six were moderately resistant, ten were susceptible, three were highly susceptible, and three were tolerant hosts of P. cinnamomi . These results indicate that field resistance recorded from mature plants may be due to asymptomatic infection or resistance may not be present in seedlings. Therefore, data from mature plants may not be appropriate when selecting species for seed-based restoration.

Species in the genus Phytophthora cause significant economic losses in crops and damage to forests and natural ecosystems worldwide. Currently, phosphite is the most effective chemical for disease management, but excessive phosphite concentrations can result in phytotoxicity in plants and the development of tolerance by the pathogen. Two newly developed metal chelates and phosphite (alone and in combination) were tested for their in vitro and in planta efficacy against Phytophthora cinnamomi. In glasshouse trials, 0.25% and 0.5% of each chemical treatment (phosphite, Ca chelate, Zn chelate) and Ca chelate + phosphite were used as a foliar application on 3-month-old seedlings of Banksia grandis (experiment not repeated) and Eucalyptus marginata, prior to inoculation with P. cinnamomi. All noninoculated control plants remained healthy, while significant root damage and reduction of dry root weights were observed for inoculated untreated plants. Individually, phosphite and Ca chelate significantly reduced root lesion development of P. cinnamomi compared to the control, with Ca chelate attaining superior results to phosphite at the same concentration. In combination, Ca chelate + phosphite had the largest reduction in root lesion development in both plant species; however, this result has not yet been replicated but did reflect previous in vitro results. The Zn chelate applications were not effective. Ca chelate has the potential to be developed as a fungicide to control Phytophthora species.

Context Forest ecosystems experience compositional and structural changes as species’ environmental envelopes shift with climate change. Extreme climate events and pests/pathogens are driving these ecosystem changes. Determining which of the two potential drivers is causing a particular forest die-off can be challenging. In south-western Australia, widespread forest die-off in 2011 coincided with extremely hot and dry conditions. It occurred in a forest ecosystem that has historically experienced Phytophthora cinnamomi root disease (Phytophthora dieback). Aims To determine whether the causal agent of Phytophthora dieback, P. cinnamomi, was associated with forest die-off in the Northern Jarrah Forest. Methods A combination of direct (isolation of pathogen) and indirect (survey of susceptible indicator plant species) measurements were taken inside and outside patches of forest experiencing the die-off. Key results There was no consistent association between die-off patches and the presence of P. cinnamomi. P. cinnamomi was isolated from 3 of 33 control plots and 3 of 33 die-off plots. Although several plant species susceptible to P. cinnamomi were absent from die-off plots, the findings were inconsistent across species. This may be explained by plant tolerance to high temperatures and drought. Conclusions P. cinnamomi was not the proximate cause of the observed die-off in the Northern Jarrah Forest in 2011. Implications Novel disturbance caused by extreme climate events can mimic damage caused by certain pests/pathogens. More research is needed to determine the tolerances of plants to extreme temperature and drought conditions to disentangle abiotic and biotic drivers of tree die-off.

AbstractClimate change is shifting temperatures from historical patterns, globally impacting forest composition and resilience. Seed germination is temperature‐sensitive, making the persistence of populations and colonization of available habitats vulnerable to warming. This study assessed germination response to temperature in foundation trees in south‐western Australia's Mediterranean‐type climate forests (Eucalyptus marginata (jarrah) and Corymbia calophylla (marri)) to estimate the thermal niche and vulnerability among populations. Seeds from the species' entire distribution were collected from 12 co‐occurring populations. Germination thermal niche was investigated using a thermal gradient plate (5–40°C). Five constant temperatures between 9 and 33°C were used to test how the germination niche (1) differs between species, (2) varies among populations, and (3) relates to the climate of origin. Germination response differed among species; jarrah had a lower optimal temperature and thermal limit than marri (To 15.3°C, 21.2°C; ED50 23.4°C, 31°C, respectively). The thermal limit for germination differed among populations within both species, yet only marri showed evidence for adaptation to thermal origins. While marri has the capacity for germination at higher thermal temperatures, jarrah is more vulnerable to global warming exceeding safety margins. This discrepancy is predicted to alter species distributions and forest composition in the future.

More Phytophthora species are detected from environmental samples through DNA metabarcoding than are isolated by baiting. We investigated whether bulking soil samples and baiting ~ 300 g samples in standard 1 L tubs resulted in the isolation of fewer Phytophthora and Phytophythium species compared with using 15 – 20 g samples of non-bulked soil in individual 200 ml tubs. At each of four sites with dying vegetation, 50 soil samples were collected and baited separately in small tubs, followed by plating of lesioned baits over 7 days. The number of Phytophthora species obtained was compared with those obtained from bulking the 50 samples and baiting subsamples in large tubs. Half of the asymptomatic baits were plated on day 7 and the remaining were assessed for the presence of Phytophthora using metabarcoding. Root samples with rhizosphere soil from the bulked soil in each site were also assessed using metabarcoding. A higher number of Phytophthora species was recovered from each site from baiting small volumes of non-bulked soil than large volumes of bulked soils. Metabarcoding of the asymptomatic baits revealed species not isolated from lesioned baits. More species were detected from the roots using metabarcoding than were isolated from baits. Metabarcoding did not reveal any species from the rhizosphere soil and roots that were not also detected from metabarcoding of the asymptomatic baits and/or plating. The numbers of Phytopythium species detected using the different methods followed the same trend as for Phytophthora . It was concluded that baiting small samples from across a site in separate small tubs results in the isolation of a higher number of Phytophthora species than the standard technique of baiting large samples of bulked soils, and that this, together with metabarcoding of asymptomatic baits, detects the highest total number of species.

Growing a high-value crop such as industrial hemp (Cannabis sativa L.) in post-mining environments is economically and environmentally attractive but faces a range of biotic and abiotic challenges. An opportunity to investigate the cultivation of C. sativa presented itself as part of post-mining activities on Christmas Island (Australia) to profitably utilise disused phosphate (PS) quarries. Challenges to plant growth and cadmium (Cd) uptake were addressed in this study using potted plants under fully controlled conditions in a growth chamber. A complete nutritional spectrum, slow-release fertiliser was applied to all plants as a control treatment, and two levels of rock PS dust, a waste product of PS mining that contains 35% phosphorus (P) and 40ppm of naturally occurring Cd, were applied at 54 and 162gL-1 . After 12weeks, control plants (no PS dust) significantly differed in phenological development, with no flower production, lower aboveground biomass and reduced photosynthesis efficiency than those with P applied as rock dust. Compared with the controls, the 54gL-1 level of P dust increased shoot biomass by 38%, while 162gL-1 increased shoot biomass by 85%. The concentration of Δ9 -tetrahydrocannabinol also increased with the higher P levels. Cd uptake from PS dust by C. sativa was substantial and warrants further investigation. However, there was no increase in Cd content between the 54 and 162gL-1 application rates in seed and leaf. Results indicate that hemp could become a high-value crop on Christmas Island, with the readily available rock PS dust providing a source of P.

Ink disease, caused by Phytophthora spp., represents a serious threat to sweet chestnuts throughout their distribution area. Among the control strategies, new perspectives have been offered by using potassium phosphonate, which indirectly controls Phytophthora diseases by acting on both host physiology and host-pathogen interactions. In this study, we tested in planta the effectiveness of trunk injection with K-phosphonate against seven different Phytophthora species associated with ink disease. For the two most aggressive species, P. cinnamomi and P. ×cambivora, the treatments were repeated at two different environmental conditions (a mean temperature of 14.5 °C vs. 25 °C) and tree phenology stages. The results obtained in this study demonstrated that K-phosphonate could contain the development of Phytophthora infection in phloem tissues. However, its effectiveness varied based on the concentration applied and the Phytophthora species tested. A concentration of 280 g/L of K-phosphonate was the most effective, and in some cases, callus formation around the necrotic lesion was detected. Overall, this study broadens the knowledge of endotherapic treatments with K-phosphonate as an effective measure for managing chestnut ink disease. Interestingly, the increase in mean temperature had a positive impact on the development of P. cinnamomi lesions on chestnut phloem tissues.

Endophytes were investigated for their potential to protect Cinnamomum cassia (cinnamon) from Phytophthora root rot. From healthy cinnamon trees in diseased plantations, 134 bacterial and fungal endophytes were isolated and screened in vitro for their ability to antagonise the root rot pathogens Phytophthora cinnamomi , P. multibullata and P. × vanyenensis . Seventeen endophytes exhibiting high levels of antagonism in vitro (more than 45%) were then tested in a glasshouse study for their ability to reduce the impact of Phytophthora infection in cinnamon seedlings. Trials using cinnamon seeds or seedlings inoculated with an endophyte and then infested with Phytophthora identified three endophytes expressing high levels of disease suppression (based on root damage reduction) and plant growth promotion. These were Penicillium citrinum , Xylaria curta and Clonostachys rosea . These endophytes can potentially be used in the biological control of root rot in cinnamon, but this must be explored further under field conditions.