Search

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.

Invasive plant species (IPS) management in national parks is a complex problem often characterized by the involvement of various organizations with different responsibilities, legal mandates, and jurisdictions. These institutional arrangements shape the structure, function, and decision-making behaviors of organizations and influence management effectiveness. Drawing on institutional theory, this study analyzed institutional arrangements and how these influenced IPS management in Vietnam’s national parks. Data were collected between May and July 2017 using in-depth interviews with 39 key informants with responsibility for IPS management at different institutional levels (national, provincial, and local national parks). Results demonstrated that IPS management in Vietnam’s national parks was characterized by centralized management with overlaps and gaps in vertical institutional relationships that limited the effectiveness of horizontal relationships. These characteristics resulted in a lack of clear guiding regulations and limited resources that restricted decision making and hindered implementation at the local national park level. The study highlights the need for a common set of principles across agencies, governed by an overarching body to promote constructive relationships across the vertical and horizontal institutional dimensions of IPS management.

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.

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.

Several species from the genus Quambalaria (order Microstromatales) cause diseases on eucalypts (Eucalyptus and related genera) both in plantations and natural ecosystems. We developed real-time quantitative PCR (qPCR) assays to rapidly detect and distinguish five Quambalaria species. The design of the species-specific qPCR assay for each species, Q. pitereka (PIT), Q. coyrecup (COR), Q. cyanescens (CYN), Q. pusilla (PUS), and Q. eucalypti (EUC), was based on the ITS region and was evaluated for specificity and sensitivity. The PIT, COR, and CYN qPCR assays could amplify as little as 10 fg µl−1 from pure cultures, whereas PUS and EUC qPCR assays could amplify 100 fg µl−1 of their target species. The PIT, COR, and CYN qPCR assays were further validated using naturally and artificially infected samples of their plant host Corymbia calophylla. These assays will be used for rapid diagnostics and future experiments on the infection process.

The health of Corymbia calophylla (marri), a keystone tree species in the native forests of southwest Western Australia, has been in decline for the past few decades. Phytophthora root disease and waterlogging have often been cited as contributing to this decline. Traditional methods (i.e., field surveys and sampling) of mapping Phytophthora root infection in the field are time-consuming and expensive; thus, the potential of reflectance spectroscopy to characterize marri response to Phytophthora and waterlogging stress was investigated. Twelve-month old marri plants were infected with either P. cinnamomi or P. multivora in two glasshouse trials and waterlogged for 24 h each fortnight. Spectral measurements with a portable high-resolution spectroradiometer were taken weekly. Plant biophysical measurements were taken at harvest time. Normalized difference spectral index (NDSI) was calculated for every combination of reflectance values between 400 and 2500 nm for all time points, correlated with the treatment effects and displayed as heat maps. Narrowband vegetation indices (VIs), utilizing different wavelengths of the electromagnetic spectrum, were also calculated from the spectral data. The Phytophthora treatments did not cause significant differences with the biophysical measurements in both trials. In the second trial, the waterlogging treatment significantly lowered plant top dry weight (P = 0.016) and diameter (P = 0.044). Reflectance values plotted against wavelength displayed differences between treatments as well as a seasonal trend. The NDSI heat maps indicated that the Phytophthora and waterlogging treatment effects were strongest correlated with bandwidths in the visible and near-infrared portions of the electromagnetic spectrum (538–558 nm and 701–709 nm). Six of the VIs (normalized difference nitrogen index 2, anthocyanin reflectance index 1, photochemical reflectance index, Carter index 1, Vogelman index 3 and water band index) were able to track the biochemical changes in the leaves over the 10 weeks, confirming the seasonal trend. The interaction effect between P. cinnamomi, waterlogging and elapsed time in the first trial was significant for water band index (P = 0.010). This study demonstrates that reflectance spectroscopy holds promise for characterizing marri response but more work needs to be done to identify the optimum wavelengths for identifying Phytophthora and waterlogging stress with marri.

Digging animals perform many ecosystem functions, including soil turnover and vectoring fungi, particularly mycorrhizal fungi. However, these animals are also susceptible to the impacts of urbanisation, resulting in altered ecosystem processes. Some digging mammals, such as the omnivorous quenda (Isoodon fusciventer), a medium-sized marsupial bandicoot endemic to southwestern Australia, persist in urban landscapes and may play important roles as fungal vectors. This paper examines the fungal community in quenda scats from natural vegetation remnants within a fragmented urban landscape to ask: are quenda acting as vectors for a functionally diverse fungal community?; what fungal functional types are being vectored?; and does remnant size impact fungal species richness and composition vectored by quenda? We sequenced 53 scat samples collected from remnants and found that quenda disperse a functionally diverse fungal community, with 31% of the molecular operational taxonomic units (OTUs) putatively mycorrhizal. Fungal OTU richness was greatest in scats from smaller remnants due to higher mean relative abundance of saprotrophs, pathogens and yeasts. Fungal OTU richness of ectomycorrhizal fungi, critical for plant growth, were found at a higher abundance in larger remnants. Fungal composition was affected by remnant size, type and condition of vegetation, and soil type. Our results indicate that maintaining digging mammal populations within urban landscapes may assist with dispersal of fungi that facilitate fungal-plant interactions, contributing to ecosystem health. These results are important to understand the complex ecological implications of urbanisation, and how remaining mammals are critical in maintaining ecosystem processes within the urban land-use matrix.

The transition from mining to agriculture is hampered by a range of abiotic challenges to crop growth, including nutritional issues and heavy metal stress. Building on our previous work showing that potassium (K) limits legume growth in post-phosphate mining substrates on tropical Christmas Island, Australia, we undertook two field trials. The first compared the efficacy of controlled release K fertilisers (CRFs: KCl 2-month release, K2SO4 3-month and K2SO4 9-month) with immediately available potassium sulfate (K2SO4) fertiliser, on the legume Lablab purpureus. The second trial tested responses of L. purpureus to different rates of K2SO4 9-month CRF, and a combination treatment (CRF and K2SO4). Both trials were undertaken to determine how CRFs compare with immediately available K2SO4 in terms of increasing biomass, reducing cadmium (Cd) concentrations, maximising plant K concentrations and maintaining K soil retention. The first trial revealed that K2SO4 3-month and 9-month CRFs were similar to the 160 kg/ha K2SO4 treatment in significantly increasing L. purpureus biomass. Plant Cd and other heavy metal concentrations were significantly lower as plant biomass increased with increasing K, including with CRFs. The second trial showed no difference between various rates of K2SO4 9-month CRF and immediately available 160 kg/ha K2SO4 to increase biomass, reduce Cd or increase K concentrations. We have shown that although post-phosphate mining substrates can limit legume growth, high biomass can be attained with some CRFs, or K2SO4 at 160 kg/ha. Optimising nutrient input in post-mining agriculture is critical for developing safe, sustainable crops.

Previous studies demonstrated that a reduction in germination of Colletotrichum alienum conidia could be achieved following treatment with cold plasma (CP) or incubation with plasma-activated water (PAW). In this study, the mode of action of CP and PAW on C. alienum conidia was explored using transmission electron microscopy. Following treatment of the conidia, noticeable ultrastructural changes were observed, including cell wall maceration, disorganization of the cytoplasm and vacuole, and changes to the nuclei and mitochondria. Disorganization of the cytoplasm was exhibited by 85% of conidia after CP or PAW treatment. Also, 85% of conidia were observed with disorganized vacuoles after 6 min of CP treatment and 65% after 3 hr incubation in PAW. Further, 45% or more conidia had modified cell walls after PAW incubation or CP treatment. Deformation of conidia was observed in 23% of conidia after PAW incubation. These ultrastructural changes are a likely reason for the reduced germination of C. alienum conidia following CP or PAW treatment.

With climate change, heat waves are becoming increasingly frequent, intense and broader in spatial extent. However, while the lethal effects of heat waves on humans are well documented, the impacts on flora are less well understood, perhaps except for crops. We summarize recent findings related to heat wave impacts including: sublethal and lethal effects at leaf and plant scales, secondary ecosystem effects, and more complex impacts such as increased heat wave frequency across all seasons, and interactions with other disturbances. We propose generalizable practical trials to quantify the critical bounding conditions of vulnerability to heat waves. Collectively, plant vulnerabilities to heat waves appear to be underappreciated and understudied, particularly with respect to understanding heat wave driven plant die-off and ecosystem tipping points.

Five new taxa from Phytophthora ITS clade 2a are described from Cinnamomum cassia plantations and adjacent waterways in Van Yen, Vietnam, disturbed rainforest in the Hela Province of Papua New Guinea and from disturbed forest on Christmas Island. Phylogenetic analyses were performed using data from nuclear regions (ITS, β-tubulin; heat shock protein 90) and mitochondrial regions (cytochrome c oxidase subunit 1; cytochrome c oxidase subunit 2; NADH dehydrogenase subunit 1; ribosomal protein L10). The molecular data supported recognition of three species: Phytophthora insulinativitatica, P. multibullata and P. x vanyenensis, and two informal taxa: P. sp. germisporangia and P. sp. awatangi. P. x vanyenensis appears to be a hybrid between P. mekongensis and an unknown species. P. multibullata and P. sp. germisporangia are phylogenetically close to P. citrophthora, but morphologically distinct. P. insulinativitatica is most closely related to P. botryosa, but has distinct morphology. P. sp. germisporangia and P. sp. awatangi were morphologically distinct and separated in the phylogeny based on mitochondrial sequences, but their nuclear sequences were identical. When comparing the sequences of these new species to that available on GenBank, it became evident that some of these species shared similarity with isolates submitted to GenBank under other species names. A re-evaluation of all P. meadii and P. colocasiae ITS sequence data identified an additional 7 putatively new species all isolated from Asia. The results support the view that many more Phytophthora species remain to be discovered in the Asia-Pacific region.

Severe tree decline in natural ecosystems around the world has driven Phytophthora research, resulting in a better understanding of the diversity and association of Phytophthora species with different host plants. Improved molecular techniques have contributed significantly to that understanding. The devastating impact of Phytophthora dieback in native vegetation in the southwest of Western Australia (SWWA) has motivated a committed research effort to understand the survival and spread of this pathogen. Hot, dry summers characterise the climate of this ecosystem, and are supposedly unfavourable for a moisture-loving pathogen to survive, spread and thrive. However, Phytophthora cinnamomi can survive within the roots of native plant species allowing for its persistence. Random plant sampling, with metabarcoding from root samples, revealed the presence of at least 23 Phytophthora species on 18 of the 20 plant species growing on mining stockpiles of the Huntly mine site (Alcoa of Australia Limited) in SWWA. Phytophthora cinnamomi was detected on 16 of the 20 plant species. This finding supports the idea that native plant species have a significant role in the survival and spread of P. cinnamomi in the environment. The presence of other Phytophthora species challenges the assumption that P. cinnamomi is the main cause of Phytophthora dieback; the disease may be complex, involving several Phytophthora species. These unexpected detections indicate that plants in the natural forest can serve as the reservoir of inoculum of not only P. cinnamomi but also for other Phytophthora species.

A diverse Phytophthora community was detected in recent surveys conducted in alpine and subalpine areas, previously considered Phytophthora free. The current study was conducted to determine patterns of Phytophthora species richness and distribution along a steep elevation gradient, and to compare these patterns with those of vascular plant species. Phytophthora and vascular plant species were recorded over a wide range of elevation gradient (410–2125 m) and across a disturbance boundary. Vascular plant species exhibited a monotonic decline with increasing elevation. With the exception of native Phytophthora species isolated by baiting, Phytophthora species richness was invariant in relation to elevation and had higher elevational ranges than vascular plant species. Vascular plants occurred in discrete plant communities with introduced species more frequently recorded in road habitat and native species more frequently recorded in natural vegetation habitat. Both native and introduced Phytophthora species occurred with equal frequency in road and natural vegetation habitat. Phytophthora species were absent from one-third of sample plots and plots with no Phytophthora species were randomly distributed across landscapes. Only two Phytophthora species repeatedly occurred with a particular plant community. Our findings show that Phytophthora species are habitat generalists, being widely distributed across elevation and disturbance gradients, while vascular plant species are mostly habitat specialists, being confined to particular environments within narrow elevation bands. The effect of Phytophthora species on vascular plant species is largely unknown but the fact that Phytophthora species are already present throughout the elevation and disturbance gradients warrants closer examination of plant-pathogen relationships.

1. Plant pathogens are introduced to new geographical regions ever more frequently as global connectivity increases. Predicting the threat they pose to plant health can be difficult without in‐depth knowledge of behaviour, distribution and spread. Here, we evaluate the potential for using biological traits and phylogeny to predict global threats from emerging pathogens. 2. We use a species‐level trait database and phylogeny for 179 Phytophthora species: oomycete pathogens impacting natural, agricultural, horticultural and forestry settings. We compile host and distribution reports for Phytophthora species across 178 countries and evaluate the power of traits, phylogeny and time since description (reflecting species‐level knowledge) to explain and predict their international transport, maximum latitude and host breadth using Bayesian phylogenetic generalised linear mixed models. 3. In the best‐performing models, traits, phylogeny and time since description together explained up to 90%, 97% and 87% of variance in number of countries reached, latitudinal limits and host range, respectively. Traits and phylogeny together explained up to 26%, 41% and 34% of variance in the number of countries reached, maximum latitude and host plant families affected, respectively, but time since description had the strongest effect. 4. Root‐attacking species were reported in more countries, and on more host plant families than foliar‐attacking species. Host generalist pathogens had thicker‐walled resting structures (stress‐tolerant oospores) and faster growth rates at their optima. Cold‐tolerant species are reported in more countries and at higher latitudes, though more accurate interspecific empirical data are needed to confirm this finding. 5. Policy implications. We evaluate the potential of an evolutionary trait‐based framework to support horizon‐scanning approaches for identifying pathogens with greater potential for global‐scale impacts. Potential future threats from Phytophthora include Phytophthora x heterohybrida, P. lactucae, P. glovera, P. x incrassata, P. amnicola and P. aquimorbida, which are recently described, possibly under‐reported species, with similar traits and/or phylogenetic proximity to other high‐impact species. Priority traits to measure for emerging species may be thermal minima, oospore wall index and growth rate at optimum temperature. Trait‐based horizon‐scanning approaches would benefit from the development of international and cross‐sectoral collaborations to deliver centralised databases incorporating pathogen distributions, traits and phylogeny.

The genus Phytophthora contains species that are major pathogens worldwide, affecting a multitude of plant species across agriculture, horticulture, forestry, and natural ecosystems. Here, we concentrate on those species that are dispersed through soil and water, attacking the roots of the plants, causing them to rot and die. The intention of this study was to compare the soil baiting protocol developed by the Centre for Phytophthora Science and Management (CPSM) with two other baiting methods used in Australia. The aim was to demonstrate the effectiveness of each protocol for soil baiting Phytophthora species in different substrates. Three experiments were conducted: the first to test the sensitivity of each method to detect Phytophthora cinnamomi, the second to test the effect of substrate type (sand or loam), and the third to test the detection of species (P. cinnamomi, P. multivora, or P. pseudocryptogea). The specificity of different plant species baits was compared within and between the methods. Substrate type influenced isolation in all methods; however, the CPSM method was superior regardless of substrate, albeit slower than one of the other methods for one substrate. Comparing bait species between the three methods, Quercus ilex was the most attractive bait for P. cinnamomi, particularly in the CPSM method. The choice of protocol affected the isolation associated with each bait type. Overall, the multiple bait system used by CPSM was shown to provide the most sensitive and reliable detection of Phytophthora species from soil samples.

In Southwestern Australia, outbreaks of cerambycids have been associated with infestation of drying and stressed trees. Felled timber provides an abundant habitat for a variety of subcortical beetles where their development can be modified by attack from natural enemies, including parasitoids. There are a variety of parasitoid wasps of cerambycids native to Australia, yet their effectiveness in controlling the larval performance of borers has been little studied. Approximately 700 Eucalyptus trees felled to realign a forest road provided an opportunity to determine how a mass of drying logs influences borer infestation rates and whether parasitoid wasps were effective in controlling borer survival. The native borer Coptocercus rubripes (Coleoptera: Cerambycidae) caused an extensive infestation of fallen trees at the clearfell site. These infestations were subsequently limited by the direct effect of parasitism from the native braconid wasps Callibracon limbatus and Syngaster lepidus emerging from a single hole in a white cocoon. The effects of parasitism showed inverse density dependency where high borer larval densities increased the chances of borer larval survival. The absence of parasitism in caged logs promoted high borer larval densities and greatly improved adult borer survival, and while this increased the demand for sapwood resources, it promoted early adult borer emergence. Control by native braconid wasps of high infestations of Co. rubripes borers attacking drying and stressed trees limits adult borer emergence and has the potential to partially regulate borer populations.

Cold plasma, an ionized gas produced by applying an electrical current to air, can be used to produce plasma‐activated water (PAW), which has excellent antimicrobial properties. In this study PAW was applied to conidia of Colletotrichum alienum to investigate its impact on conidial germination in vitro. PAW was produced by treating tap, deionized, or distilled water with cold plasma for 30 or 60 min to produce PAW30 or PAW60, each of which was then incubated for up to 24 hr with a conidial suspension of C. alienum in a ratio of 1:1, 1:2, or 1:3 (conidial suspension:PAW), and the percentage germination measured. The greatest reduction in germination occurred when conidia were incubated with PAW60 produced from deionized water or distilled water, for all ratios. For PAW30, deionized water was the most effective for all three ratios, and on this basis, deionized water was selected for all further experiments. PAW produced from smaller volumes of water and at shorter distances from the cold plasma source was more effective at reducing germination. Treatment of conidia with acidified water was not as effective as PAW at inhibiting germination. Nitrates and nitrites were present in the PAW in varying concentrations and may have contributed to the inhibition of germination. PAW retained activity and reduced germination even after storage for 15 days. These findings demonstrate the potential of PAW as a novel treatment for postharvest fungal pathogens.

Diseases caused by pathogens, alone or in combination with other stress factors, are a major threat to the future health of urban forests. Root diseases caused by Phytophthora species are frequently evident in urban environments due to conducive environments for these pathogens, and to conditions predisposing trees to attack. Urban environments are also an important pathway for the introduction of Phytophthora species into novel ecosystems. We have detected many different Phytophthora species from dying and declining trees in the urban and peri-urban environment, and for many of these species, little is known about their host range. Therefore, the aim of this study was to examine the host range of 19 Phytophthora species, including many recently described species, against fifteen tree species commonly used in urban plantings in Perth, Western Australia. Excised branches of each tree species were under-bark inoculated with each Phytophthora species, incubated and lesions were measured after 8 days. Six Phytophthora species were pathogenic to all fifteen-tree species, with ~75% of the species each causing disease in ≥85% of plant hosts. All Phytophthora species formed lesions in Eucalyptus marginata and Corymbia calophylla. Phytophthora cinnamomi, P. pseudocryptogea, and P. citrophthora were the most pathogenic species causing the largest lesions in most of these trees species. It is likely many of these Phytophthora species have a negative impact on the health of urban forests where they are present.

DNA and RNA detected in soil using molecular techniques may originate from a living or dead organism. It is therefore of interest to know how long the DNA and RNA from a decaying organism can persist in soil, and how environmental conditions such as soil temperature, moisture, and microbial populations impact on the survival time. This study determined the difference between the persistence of Phytophthora cinnamomi mRNA and DNA in different soil types. DNA and RNA were extracted from P. cinnamomi and 10 ng/250 mg of soil was applied to five different soil types that were either air‐dried or maintained at 70% field capacity. The persistence of DNA at 20°C was tested after intervals of 0, 3, 7, 14, 90, 241, and 378 days, and for RNA at 0, 1, 3, and 7 days using qPCR and RT‐qPCR techniques, respectively. Persistence was longer in dry than moist soil, P. cinnamomi DNA could be readily detected in dry soil conditions for up to 90 days and was found at extremely low levels at 241 and 378 days. RNA was detected only on day 1, except for dry river sand, and moist sandy loam in which it persisted for 3 days; it was not detected after seven days. These results confirm that RNA degrades very quickly, making it a valuable tool for determining the presence of viable Phytophthora in soil. In contrast, DNA can be remarkably stable in some environments, and positive results could be obtained even after the death of the organism for a year or more prior to the test. For diagnostics, the use of an RNA‐based test avoids the possibility of such false positive results. In the context of the research project, this study is relevant to determining how long viable Phytophthora remains in soil after the eradication protocols have been instigated. In a broader context, the persistence of DNA is relevant to any study using environmental DNA for diagnostics or for metabarcoding when undertaking community ecology or microbiome studies. These results are relevant for studies using detection of P. cinnamomi nucleic acids in soils for purposes of diagnostics, ecological research, or projects on eradication.

Many recently described Phytophthora species detected using high‐throughput sequencing have never been isolated into culture. NARH is a commonly used isolation medium containing cornmeal agar with nystatin 22.72 ppm, ampicillin 100 ppm, rifampicin 10 ppm, and hymexazol 50 ppm. We investigated whether the antimicrobial compounds in this medium selectively inhibit growth of some Phytophthora species. Growth of 10 Phytophthora species from 10 Phytophthora clades was tested in NARH medium with antimicrobials in a range of concentrations, singly and in combination: nystatin 12.5–100 ppm, ampicillin 62.5–500 ppm, rifampicin 5–40 ppm, hymexazol 12.5–100 ppm and in addition, chloramphenicol 5–40 ppm. Two combinations of antimicrobials that supported good growth of the greatest number of species were selected: (a) nystatin 12.5 ppm, ampicillin 250 ppm, rifampicin 10 ppm, and hymexazol 12.5 ppm, and (b) these compounds with the addition of chloramphenicol 5 ppm. Subsequently the growth of 47 Phytophthora species from all clades was tested in media with these two combinations and standard NARH, both in aseptic culture and in plates with leaf baits infected from soils known to be infested with Phytophthora . Although growth of some Phytophthora species was better with the new combinations of antimicrobials in aseptic culture, suppression of competing microorganisms was best in standard NARH. Sensitivity to the NARH antimicrobials is not the reason for the difficulty or failure of isolating many species detected using high‐throughput sequencing. NARH is a robust and appropriate medium for isolation of Phytophthora species from all clades.

Phytophthora cinnamomi has recently been found in highly diverse and fragile alpine and sub-alpine environments previously considered P. cinnamomi and disease free due to low temperatures. In the laboratory, we investigated the ability of P. cinnamomi isolates to adapt to cold and cause disease under conditions comparable to alpine and sub-alpine environments. Initially, the ability of P. cinnamomi isolates to produce sporangia at 10 °C (2 °C lower than previously reported in the literature) was demonstrated in vitro. The lowest temperature limit for host infection was determined (i.e., 8 °C) and the phenotypic plasticity of isolates was then explored in planta in two successive phenotypic plasticity experiments comparing cold 9, 7.5 °C, and ambient temperature 25 (±5 °C). In the phenotypic plasticity experiment-1, three of the five isolates recovered from plants grown at 9 °C produced sporangia and released zoospores (infective propagules) at 7.5 °C, even lower than determined initially, i.e., 10 °C. No changes were observed in the same set of isolates recovered from plants grown at ambient temperature in the glasshouse as a control, which shows that P. cinnamomi can exhibit phenotypic plasticity and responds rapidly to selection pressure and adapts to new environments. Although P. cinnamomi isolates could produce infective propagules at 7.5 °C in vitro, they could not be recovered from inoculated plants grown at 7.5 °C after 3 months in phenotypic plasticity experiment-2. More work is, therefore, needed to establish disease development by P. cinnamomi at 7.5 °C and below.

Quambalaria shoot blight (QSB) has emerged recently as a severe disease of Corymbia calophylla (marri). In this study, QSB damage and growth were assessed in Corymbia calophylla trees at 4 and 6 years of age in two common gardens consisting of 165 and 170 open-pollinated families representing 18 provenances across the species’ natural distribution. There were significant differences between provenances for all traits. The narrow-sense heritability for growth traits and QSB damage at both sites were low to moderate. The genetic correlation between QSB damage and growth traits was negative; fast-growing families were less damaged by QSB disease. Age-age genetic correlations for individual traits at four and six years were very strong, and the type-B (site–site) correlations were strongly positive for all traits. Provenances from cooler wetter regions showed higher resistance to QSB. The QSB incidence at 6 years was significantly correlated with environmental factors of the provenance’s origin. The QSB incidence at years four and six was not correlated with the QSB expression in 3-month-old seedlings. Based on these results, selection for resistance could be undertaken using 4-year-old trees. There is potential for a resistance breeding program to develop populations of marri genetically diverse and resistant to QSB.

Even though survival rates for mangrove restoration in Vietnam have often been low, there is no information on fungal pathogens associated with mangrove decline in Vietnam. Therefore, this research was undertaken to assess the overall health of mangrove afforestation in Thanh Hoa Province and fungal pathogens associated with tree decline. From a survey of 4800 Sonneratia trees, the incidence of disorders was in the order of pink leaf spot &gt, shoot dieback &gt, black leaf spot for S. caseolaris and black leaf spot &gt, pink leaf spot for S. apetala. Approximately 12% of S. caseolaris trees had both pink leaf spot and shoot dieback, while only 2% of S. apetala trees had black leaf spot and shoot dieback. Stem and leaf samples were taken from symptomatic trees and fungi were cultured in vitro. From ITS4 and ITS5 analysis, four main fungal genera causing leaf spots and shoot dieback on the two Sonneratia species were identified. The most frequently isolated fungal taxa were Curvularia aff. tsudae (from black leaf spot),Neopestalotiopsis sp.1 (from stem dieback), Pestalotiopsis sp.1 (from pink leaf spot), and Pestalotiopsis sp.4a (from black leaf spot). The pathogenicity of the four isolates was assessed by under-bark inoculation of S. apetala and S. caseolaris seedlings in a nursery in Thai Binh Province. All isolates caused stem lesions, and Neopestalotiopsis sp.1 was the most pathogenic. Thus, investigation of fungal pathogens and their impact on mangrove health should be extended to other afforestation projects in the region, and options for disease management need to be developed for mangrove nurseries.

A global database of the pathogen genus Phytophthora, comprising ca. 12,500 disease reports over 142 years, was collated to benchmark and examine the genus-wide distribution and invasiveness. Rarefaction was used to estimate global Phytophthora species richness. We applied a framework, leveraging geographically and economically biased pathogen data against environmental and socioeconomic metrics to model their distribution. Hierarchical clustering of host and country range allowed characterisation of invasion potential. Phytophthora descriptions rose to 86 by the year 2000, surging to over 180 species to date driven primarily by novel molecular techniques, resulting in a species richness estimate of 326 (95% CI: 274–378). Countries with diverse ecosystems and entrenched agricultural and forestry industries supported by intensive research programmes reported the highest diversity. Constructing principal components from enviro-socioeconomic factors highlighted national data deficits, showing that two-thirds of trading nations have reported lower-than-predicted species numbers. Phytophthora species clustered into two main invasiveness groups as either cosmopolitan generalists or specialists, historically tied to agriculture. Further spread and detection of Phytophthora pathogens are inevitable with increasing global trade, especially in developing and emerging economies. Adoption of best practice diagnostics and enhanced resource and data sharing are crucial for coordinated global pathogen surveillance and biosecurity. This research aimed to test the following hypotheses: • The global distribution of Phytophthora species is associated with environmental, social and economic traits of different country’s. • Models for Phytophthora diversity, incorporating environmental, social and economic characteristics, can be used to predict a countries trade risk. • Phytophthora species biogeography and host range can be used to predict invasiveness and a country’s conduciveness to infection.

Worldwide, extreme climatic events such as drought and heatwaves are associated with forest mortality. However, the precise drivers of tree mortality at individual and stand levels vary considerably, with substantial gaps in knowledge across studies in biomes and continents. In 2010–2011, a drought‐associated heatwave occurred in south‐western Australia and drove sudden and rapid forest canopy collapse. Working in the Northern Jarrah (Eucalyptus marginata) Forest, we quantified the response of key overstory (E. marginata, Corymbia calophylla) and midstory (Banksia grandis, Allocasuarina fraseriana) tree species to the extreme climate event. Using transects spanning a gradient of drought impacts (minimal (50–100 m), transitional (100–150 m) and severe (30–60 m)), tree species mortality in relation to stand characteristics (stand basal area and stem density) and edaphic factors (soil depth) was determined. We show differential mortality between the two overstory species and the two midstory species corresponding to the drought‐associated heatwave. The dominant overstory species, E. marginata, had significantly higher mortality (~19%) than C. calophylla (~7%) in the severe zone. The midstory species, B. grandis, demonstrated substantially higher mortality (~59%) than A. fraseriana (~4%) in the transitional zone. Banksia grandis exhibited a substantial shift in structure in response to the drought‐associated heatwave in relation to tree size, basal area and soil depth. This study illustrates the role of climate extremes in driving ecosystem change and highlights the critical need to identify and quantify the resulting impact to help predict future forest die‐off events and to underpin forest management and conservation.

Phytophthora cinnamomi causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (cox2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against P. cinnamomi and two closely related clade 7 species, P. parvispora and P. niederhauseri. From these tests, five primer pairs were selected based on specificity and, with a species-specific P. cinnamomi probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 Phytophthora isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of P. cinnamomi DNA and showed no cross-reaction with other Phytophthora species, except for P. parvispora, a very closely related species to P. cinnamomi, which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with P. cinnamomi. Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of P. cinnamomi in recalcitrant environmental samples.

Natural ecosystems are under pressure from increasing abiotic and biotic stressors, including climate change and novel pathogens, which are putting species at risk of local extinction, and altering community structure, composition and function. Here, we aim to assess adaptive variation in growth and fungal disease resistance within a foundation tree, Corymbia calophylla to determine local adaptation, trait heritability and genetic constraints in adapting to future environments. Two experimental planting sites were established in regions of contrasting rainfall with seed families from 18 populations capturing a wide range of climate origins (~4,000 individuals at each site). Every individual was measured in 2015 and 2016 for growth (height, basal diameter) and disease resistance to a recently introduced leaf blight pathogen (Quambalaria pitereka). Narrow‐sense heritability was estimated along with trait covariation. Trait variation was regressed against climate‐of‐origin, and multivariate models were used to develop predictive maps of growth and disease resistance. Growth and blight resistance traits differed significantly among populations, and these differences were consistent between experimental sites and sampling years. Growth and blight resistance were heritable, and comparisons between trait differentiation (Q ST) and genetic differentiation (F ST) revealed that population differences in height and blight resistance traits are due to divergent natural selection. Traits were significantly correlated with climate‐of‐origin, with cool and wet populations showing the highest levels of growth and blight resistance. These results provide evidence that plants have adaptive growth strategies and pathogen defence strategies. Indeed, the presence of standing genetic variation and trait heritability of growth and blight resistance provide capacity to respond to novel, external pressures. The integration of genetic variation into adaptive management strategies, such as assisted gene migration and seed sourcing, may be used to provide greater resilience for natural ecosystems to both biotic and abiotic stressors.

Several species from the genus

Actinomycetes isolated from carrot rhizosphere were screened for their in vitro and in vivo antagonism to Pythium coloration Vaartaja, a causal agent of cavity-spot disease of carrots (Daucus carata L.). Forty-five streptomycete and non-streptomycete actinomycete isolates were screened for in vitro antagonism in a carrot bioassay. Of these, seven which reduced or prevented lesion formation were identified using cultural, morphological, physiological, biochemical and cell wall characteristics as Streptomyces janthimts, S. cinerochromogenes, Streptoverticilium netropsis, Actinomadura rubra, Actinoplanes philippinensis, Muromonospora carbonaceae, and Streptosporangium albidum. All seven isolates tested produced non-volatile antifungal metabolites, but failed to produce inhibitory volatile compounds. Actinoplanef philippincnsis and M. carbonacea grew epiphytically on the hyphae and oospores of P. eoloratum. The external surface of the oospores of the pathogen was heavily colonized by both hyperparasites, their hyphae were found to coil tightly around the oospore wall, and frequently caused cytoplasmic collapse of oospores. Sporangia of A. philippinensis were often seen to emerge from the colonized hyphae and oospores of P. eoloratum. None of the other actinomycete isolates showed hyperparasitism. All seven isolates significantly reduced the incidence of cavity spot in soil artificially infested with the pathogen in the glasshouse. Streptomyces janlhinus and Stfepto. albidum were the most effective in reducing the disease in inoculated plants. In addition, all the actinomycetes species except Ac. rubra and M. carbonacea, in the presence or absence of the pathogen, significantly (P < 0.05) increased mean fresh root weight compared to the treatment which included P. thorium only. This study shows that these actinomycetes have considerable potential for future use as biocontrol agents of cavity spot under natural field conditions. This is the first report of cavity-spot disease of carrots being controlled by microbial antagonists, and is the first report of non-streptomycete actinomycetes to control a Pythium disease.

Significant portions of the world's forests have been impacted by severe and large‐scale tree declines characterised by gradual but widespread loss of vigour and subsequent death of either single or several tree species. Tree deaths represent a threat for fauna that are dependent on forest habitats for their survival. Although tree declines have received considerable scientific attention, surprisingly, little is known about their impacts on fauna. In total, we calculated 631 effect sizes across 59 studies that quantified the impact of tree declines on animal abundance. Data representing 186 bird species indicated an overall increase in bird abundance in response to tree declines (meta‐analysis mean ± estimation g = 0.172 ± 0.053 [CI 0.069 to 0.275], P = 0.001); however, there was substantial variability in responses (significant heterogeneity P

In forest ecosystems, habitat fragmentation negatively impacts stand structure and biodiversity; the resulting fragmented patches of forest have distinct, disturbed edge habitats that experience different environmental conditions than the interiors of the fragments. In southwest Western Australia, there is a large-scale decline of the keystone tree species Corymbia calophylla following fragmentation and land use change. These changes have altered stand structure and increased their susceptibility to an endemic fungal pathogen, Quambalaria coyrecup, which causes chronic canker disease especially along disturbed forest habitats. However, the impacts of fragmentation on belowground processes in this system are not well-understood. We examined the effects of fragmentation on abiotic soil properties and ectomycorrhizal (ECM) and arbuscular mycorrhizal (AM) fungal communities, and whether these belowground changes were drivers of disease incidence. We collected soil from 17 sites across the distribution range of C. calophylla. Soils were collected across a gradient from disturbed, diseased areas to undisturbed, disease-free areas. We analysed soil nutrients and grew C. calophylla plants as a bioassay host. Plants were harvested and roots collected after 6 months of growth. DNA was extracted from the roots, amplified using fungal specific primers and sequenced using Illumina MiSeq. Concentrations of key soil nutrients such as nitrogen, phosphorus and potassium were much higher along the disturbed, diseased edges in comparison to undisturbed areas. Disturbance altered the community composition of ECM and AM fungi; however, only ECM fungal communities had lower rarefied richness and diversity along the disturbed, diseased areas compared to undisturbed areas. Accounting for effects of disturbance, ECM fungal diversity and leaf litter depth were highly correlated with increased disease incidence in C. calophylla. In the face of global change, increased virulence of an endemic pathogen has emerged in this Mediterranean-type forest.

The mode of persistence of Phytophthora cinnamomi, a highly aggressive soil‐ and water‐borne pathogen, remains unclear. This study investigated the survival of viable oospores and chlamydospores of P. cinnamomi when present as free propagules in untreated soil, or in soil subject to four exogenous treatments: smoke water, fish emulsion and two fungicides (ridomil and furalaxyl). The exogenous treatments were applied under moist and dry soil conditions. Spore viability was determined by the thiazolyl blue tetrazolium bromide (MTT) staining technique, with a qPCR assay used to compare general patterns of decline. Over 96% of oospores lost viability over a period of 48 weeks irrespective of soil moisture conditions. The mean percentage viability for oospores decreased from 91% at time zero to 72, 35, 20 and 1% after 6, 12, 24 and 48 weeks, respectively. Reduction in viability of chlamydospores was more rapid than oospores, with viability declining from 92% to zero after 12 weeks. There was no significant difference between untreated soil and the exogenous treatments. The RNA‐based qPCR assay indicated a strong presence of viable oospores of P. cinnamomi up to week 12 for moist soil and week 3 for dry soil, but thereafter failed to detect RNA even though viable oospores could be detected by MTT staining. Based on the MTT staining, this study indicated that viability of P. cinnamomi oospores may be entirely lost within 1 year and that of chlamydospores within 3 months for the soil type tested. Therefore, oospores and chlamydospores when existing as free propagules in soil appear unlikely to be involved in the long‐term survival of P. cinnamomi.

The Australian Research Council (Linkage Project 120200581) and conducted within the Western Australian State Centre of Excellence for Climate Change Woodland and Forest Health, which is a partnership between private industry, community groups, universities and the Government of Western Australia.

Bioturbation is an important ecosystem process, and the loss of native digging mammals due to introduced predators and habitat loss may have detrimental consequences for ecosystem health. The mycophagous woylie (Bettongia penicillata ogilbyi) was once widespread across the Australian continent and currently exists in a greatly reduced range, while the omnivorous quenda (Isoodon fusciventer), which once occurred across the southern part of Western Australia (WA), remains common in south west WA over a reduced range. Populations of these two digging marsupials are currently maintained within sanctuaries where they can reach high densities. To assess the influence these digging marsupials have on fungal assemblages, we investigated fungal root associations among seedlings of a key mycorrhizal forest canopy species, Corymbia calophylla, R. Br. K. D. Hill and L. A. S. Johnson. Seedlings were grown in soil collected from inside (heavily-dug soil) and outside (minimally-dug soil) two predator-proof sanctuaries. Our results showed that above-ground seedling biomass was significantly greater for seedlings grown in soil collected from inside the sanctuaries. There were no differences in the diversity or species richness of rhizosphere fungal communities isolated from these seedlings; however, the community composition was significantly different. This was most obvious for the predator-proof enclosure that had been in place for 20 years (Karakamia Sanctuary) compared with the more recently-installed Perup Sanctuary (fenced in 2010; 4 years before this study). At Karakamia, there were greater numbers of putatively hypogeous ectomycorrhizal fungi inside the enclosure and four times the number of operational taxonomic units of arbuscular mycorrhizal fungi outside the enclosure. The differences in fungal communities suggest that digging mammals play a pivotal role in ecosystem functioning by influencing the rhizosphere of this key forest canopy species, which has implications for maintaining the health and persistence of forests.

Understanding the factors, or filters, that preclude the recolonization of, and population persistence in, restoration areas by fauna is important for maximizing the biodiversity benefits of restoration. We investigated filters through a long-term study examining reptile and mammal recolonization of, and population persistence in, post-mining restoration in the northern jarrah forest of southwestern Australia. Neither mammal community composition, nor individual mammal species, differed between unmined forest and restoration but reptile communities did and some reptile species were significantly less abundant in restoration than in unmined forest. We concluded that there were no filters to mammal recolonization and persistence but that there were both unidirectional (decreasing gradually over time) and dynamic (fluctuating over time) filters to reptile recolonization of post-mining restoration that influenced both recolonization and population persistence of some reptile species. Low volumes of coarse woody debris appeared to be a unidirectional filter that will slow recolonization by some reptile species for decades or even centuries. Canopy cover appeared to be a dynamic filter that fluctuated over a period of >7 years and precluded population persistence of some reptile species that had already recolonized the post-mining restoration. A dearth of studies made it difficult to generalize how widespread these filters were in restoration areas but studies of thinning and burning in natural forests suggested they were likely to be widespread. Although management techniques to reduce the effect of unidirectional and dynamic filters remain poorly developed, their development and adoption will improve the ability of restoration to facilitate fauna recolonization and persistence and better contribute towards biodiversity conservation.

Globally, land-use transition from mining to agriculture is becoming increasingly attractive and necessary for many reasons. However, low levels of necessary plant nutrients, and high levels of heavy metals, can hamper plant growth, affecting yield, and potentially, food safety. In post-phosphate mining substrates, for example, nitrogen (N) is a key limiting nutrient, and, although legumes are planted prior to cereals, N supplementation is still necessary. We undertook two field trials on Christmas Island, Australia, to determine whether Sorghum bicolor could be grown successfully in a post-phosphate mining substrate. The first trial investigated N (urea) demand (amount of N required for adequate crop growth) for S. bicolor, and whether N addition could reduce the naturally occurring cadmium (Cd) concentrations in the crop. The second trial examined whether slow release nitrogen fertilizers (SRF) could replace urea to increase biomass and reduce Cd concentrations. Our first trial demonstrated that S. bicolor has a high N demand, with the highest biomass being recorded in the 160kg/ha urea treatment. However, plants treated with 80, 120 and 160kg/ha were not significantly different from one another. After 7weeks of growth, leaf Cd concentrations were significantly lower for all urea treatments compared with the control plants. However, after 23weeks, seed Cd concentrations did not differ across treatments. Our second trial demonstrated that the application of SRF (Macracote® and Sulsync®) and 160kg/ha urea significantly increased biomass above the control plants. There was, however, no treatment response in terms of Cd or N concentrations in the seed at final harvest. Thus, we have shown that N is currently critical for S. bicolor, even following legume cropping, and that high biomass and a significant reduction in Cd can be attained with appropriate levels of urea. Our work has important implications for cereal growth and food safety in post-mining agriculture.

Mycorrhizal fungi serve important functions in Australian ecosystems by forming mutualistic symbioses with plants that facilitate water and nutrient uptake. Scat analyses have shown that southern brown bandicoots (Isoodon obesulus fusciventer; 'Quenda') regularly feed on fungi, including ectomycorrhizal (ECM) species. Many of these ECM species are hypogeous and rely on mycophagous animals such as quenda to disperse their spores. We explored the tripartite relationship between a keystone Mediterranean tree, its associated mycorrhizal fungi, and a mammalian disperser. Wild-collected quenda scats were used as a mycorrhizal inoculum to grow Eucalyptus gomphocephala from seeds under glasshouse conditions. Autoclaved scats were used as a negative-control and sporocarp tissue from Pisolithus and Scleroderma ectomycorrhizal species were mixed together as a positive-control inoculum. Seedlings were harvested at 10 weeks to assess seedling growth and early mycorrhizal colonization of roots by high-throughput DNA sequencing. Quenda scat successfully introduced fungi to seedlings, shown by a 56% overlap of fungal operational taxonomic units (OTUs) detected in the scats and roots grown in fresh scat inoculum. Scat-inoculated seedlings had richer root mycorrhiza fungal assemblages and a higher proportion of mycorrhizal taxa compared to negative- and positive-controls. However, no difference in shoot or root mass in these young seedlings could be attributed to root fungi assemblages at this early growth stage, possibly reflecting that the role of mycorrhizae in these early seedlings was parasitic, rather than facilitatory. Our study has shown that spores of mycorrhizal fungi from the quenda scat inoculum can successfully germinate and colonize seedling roots after passage through the quenda gut.

We used molecular profiling with 454 pyrosequencing to identify ectomycorrhizal, arbuscular mycorrhizal fungi, and other fungal communities associated with containerized Eucalyptus gomphocephala seedling roots. We found a higher proportion of ectomycorrizal fungi associated with seedling roots grown in soil collected from sites with healthy trees, and of arbuscular mycorrhizal fungi from seedling roots grown in soil collected from sites with declining trees. We also found a relatively high proportion of pathogenic fungi present in roots from declining sites compared to healthy sites. This research should be extended to the field to further investigate mycorrhizal and pathogenic fungal populations associated with tree declines.

A detailed site investigation of a eucalypt nursery suffering disease losses revealed the causal agent to be Phytophthora boodjera. The pathogen was detected in vegetation surrounding the nursery production area, including the lawn, under the production benches during the growing season, and, most importantly, from plant debris in used trays. However, it was not found in the container substrate, water supplies, or production equipment or on the workers themselves. The sterilization methods used by the nursery were shown to be ineffective, indicating that a more rigorous method was required. Boiling trays for 15 min or steaming at 65°C for 60 min eradicated P. boodjera. This pathogen was more pathogenic to the eucalypts tested in their early seedling stage than P. cinnamomi. Tracing of out-planting to revegetation sites showed that P. boodjera was able to spread into the environment. Dispersal via out-planting to native vegetation may affect seedling recruitment and drive long-term shifts in native plant species. Inadequate nursery hygiene increases the risk of an outbreak and can limit the success of biosecurity efforts as well as damage conservation efforts.