Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem

Phytopathogenic oomycetes constitute some of the most devastating plant pathogens and cause significant crop and horticultural yield and economic losses. The phytopathogen Phytophthora cinnamomi causes dieback disease in native vegetation and several crops. The most commonly used chemical to control P. cinnamomi is the oomyceticide phosphite. Despite its widespread use, the mode of action of phosphite is not well understood and it is unclear whether it targets the pathogen, the host, or both. Resistance to phosphite is emerging in P. cinnamomi isolates and other oomycete phytopathogens. The mode of action of phosphite on phosphite-sensitive and resistant isolates of the pathogen and through a model host was investigated using label-free quantitative proteomics. In vitro treatment of sensitive P. cinnamomi isolates with phosphite hinders growth by interfering with metabolism, signalling and gene expression; traits that are not observed in the resistant isolate. When the model host Lupinus angustifolius was treated with phosphite, proteins associated with photosynthesis, carbon fixation and lipid metabolism in the host were enriched. Increased production of defence-related proteins was also observed in the plant. We hypothesise the multi-modal action of phosphite and present two models constructed using comparative proteomics that demonstrate mechanisms of pathogen and host responses to phosphite. SIGNIFICANCE: Phytophthora cinnamomi is a significant phytopathogenic oomycete that causes root rot (dieback) in a number of horticultural crops and a vast range of native vegetation. Historically, areas infected with phosphite have been treated with the oomyceticide phosphite despite its unknown mode of action. Additionally, overuse of phosphite has driven the emergence of phosphite-resistant isolates of the pathogen. We conducted a comparative proteomic study of a sensitive and resistant isolate of P. cinnamomi in response to treatment with phosphite, and the response of a model host, Lupinus angustifolius, to phosphite and its implications on infection. The present study has allowed for a deeper understanding of the bimodal action of phosphite, suggested potential biochemical factors contributing to chemical resistance in P. cinnamomi, and unveiled possible drivers of phosphite-induced host plant immunity to the pathogen.

Host range of Phytophthora spp. from berry crops in Huelva, Spain

Crop declines have been observed in raspberry and blueberry farms in the southwest region of Spain, which is the most important berry-producing area in the country. This study aimed to identify and characterize the pathogens associated with these diseases using molecular and morphological methods. Additionally, pathogenicity tests were performed on different raspberry, blueberry, and strawberry cultivars to determine possible susceptible hosts in the area. An isolate of P. cactorum was obtained from a symptomatic strawberry plant, an isolate of P. cinnamomi was obtained from a symptomatic blueberry plant, and isolates identified as P. rosacearum, P. rubi and a previously unknow speciesrecently named as P. sp. balkanensis were recovered from symptomatic raspberry plants. Results from the pathogenicity tests reported, for the first time, P. rubi causing root rot and wilting complex (RRWC) in Spanish raspberry crops. Additionally, P. cinnamomi was found to affect highbush blueberry production in Spain. Thus, this study provides valuable insights into the identification and characterization of Phytophthora spp. associated with the decline of blueberry and raspberry crops in Huelva. It also provides essential recommendations regarding the potential risks associated with the use of other types of berries as rotational crops and emphasizes the necessity for effective management strategies to mitigate crop losses. This is particularly critical given the limited soil disinfection alternatives available in Spain.

Resistance induction with silicon in Hass avocado plants inoculated with Phytophthora cinnamomi Rands

Root rot caused by Phytophthora cinnamomi Rands, is one of the main factors that limits avocado production worldwide; silicon as a defense inducer seems to be a viable strategy to integrate into the management of this disease. Hereby, the present study evaluated the induction of resistance with silicon in Hass avocado plants inoculated with P. cinnamomi, as a possible alternative to conventional agrochemical management. A potassium silicate solution (10 mL, 0.2 M expressed as SiO₂) was applied by irrigation, for ten days before inoculation with P. cinnamomi in Hass avocado plants. Leaf samples were taken at 3, 24, 144, and 312 h after inoculation with the pathogen. Peroxidase (POD) and polyphenol oxidase (PPO) enzymes had their highest activity 3 h after pathogen inoculation (p < .05). There was a decrease in the activity of the enzyme phenylalanine ammonialyase (PAL), in the content of total phenols, and the inhibition capacity of the DPPH^● radical, between 3 h and 24 h in the plants with the inducer and inoculated with P. cinnamomi (p < .05). The results suggest a beneficial effect of silicon as a defense inducer in Hass avocado plants, manifested in the activation of enzymatic pathways related to the regulation of oxidative stress and the synthesis of structural components. Therefore, the application of silicon as a defense inducer emerges as a strategy to include in the integrated management of the disease caused by P. cinnamomi in Hass avocado.

Post-Transcriptional Gene Silencing of Glucanase Inhibitor Protein in Phytophthora cinnamomi

Ink disease is considered one of the most significant causes contributing to the decline of chestnut orchards. The reduced yield of Castanea sativa Mill can be attributed to two main species: Phytophthora cinnamomi and Phytophthora cambivora, with the first being the main pathogen responsible for ink disease in Portugal. P. cinnamomi is a highly aggressive and widely distributed plant pathogen, capable of infecting nearly 1000 host species. This oomycete causes substantial economic losses and is accountable for the decline of numerous plant species in Europe and worldwide. To date, no effective treatments are available to combat these pathogens. Given chestnut's economic and ecological significance, particularly in Portugal, it is crucial to investigate the molecular mechanisms underlying the interaction between Phytophthora species and host plants. This can be achieved through the study of the glucanase inhibitor protein (GIP) produced by P. cinnamomi during infection. The technique of RNA interference (RNAi) was employed to suppress the GIP gene of P. cinnamomi. The resulting transformants, carrying the silenced gene, were used to infect C. sativa, allowing for the assessment of the effects of gene silencing on the plant's phenotype. Additionally, bioinformatics tools predicted the secretion of GIP protein. The obtained results validate RNAi as a potential alternative tool for studying molecular factors and for controlling and managing P. cinnamomi.

The expression of the NPR1-dependent defense response pathway genes in Persea americana (Mill.) following infection with Phytophthora cinnamomi

A plant's defense against pathogens involves an extensive set of phytohormone regulated defense signaling pathways. The salicylic acid (SA)-signaling pathway is one of the most well-studied in plant defense. The bulk of SA-related defense gene expression and the subsequent establishment of systemic acquired resistance (SAR) is dependent on the nonexpressor of pathogenesis-related genes 1 (NPR1). Therefore, understanding the NPR1 pathway and all its associations has the potential to provide valuable insights into defense against pathogens. The causal agent of Phytophthora root rot (PRR), Phytophthora cinnamomi, is of particular importance to the avocado (Persea americana) industry, which encounters considerable economic losses on account of this pathogen each year. Furthermore, P. cinnamomi is a hemibiotrophic pathogen, suggesting that the SA-signaling pathway plays an essential role in the initial defense response. Therefore, the NPR1 pathway which regulates downstream SA-induced gene expression would be instrumental in defense against P. cinnamomi. Thus, we identified 92 NPR1 pathway-associated orthologs from the P. americana West Indian pure accession genome and interrogated their expression following P. cinnamomi inoculation, using RNA-sequencing data. In total, 64 and 51 NPR1 pathway-associated genes were temporally regulated in the partially resistant (Dusa®) and susceptible (R0.12) P. americana rootstocks, respectively. Furthermore, 42 NPR1 pathway-associated genes were differentially regulated when comparing Dusa® to R0.12. Although this study suggests that SAR was established successfully in both rootstocks, the evidence presented indicated that Dusa® suppressed SA-signaling more effectively following the induction of SAR. Additionally, contrary to Dusa®, data from R0.12 suggested a substantial lack of SA- and NPR1-related defense gene expression during some of the earliest time-points following P. cinnamomi inoculation. This study represents the most comprehensive investigation of the SA-induced, NPR1-dependent pathway in P. americana to date. Lastly, this work provides novel insights into the likely mechanisms governing P. cinnamomi resistance in P. americana.

God save the queen! How and why the dominant evergreen species of the Mediterranean Basin is declining?

Quercus ilex may be considered the queen tree of the Mediterranean Basin, dominating coastal forest areas up to 2000 m above sea level at some sites. However, an increase in holm oak decline has been observed in the last decade. In this review, we analysed the current literature to answer the following questions: what are the traits that allow holm oak to thrive in the Mediterranean environment, and what are the main factors that are currently weakening this species? In this framework, we attempt to answer these questions by proposing a triangle as a graphical summary. The first vertex focuses on the main morpho-anatomical, biochemical and physiological traits that allow holm oak to dominate Mediterranean forests. The other two vertices consider abiotic and biotic stressors that are closely related to holm oak decline. Here, we discuss the current evidence of holm oak responses to abiotic and biotic stresses and propose a possible solution to its decline through adequate forest management choices, thus allowing the species to maintain its ecological domain.

Temperature and Fungicide Sensitivity in Three Prevalent Phytophthora Species Causing Phytophthora Root Rot in Rhododendron

Temperature is an important environmental variable affecting Phytophthora spp. biology. It alters the ability of species to grow, sporulate, and infect their plant host, and it is also important in mediating pathogen responses to disease control measures. Average global temperatures are increasing as a consequence of climate change, yet there are few studies that compare the effects of temperature on Phytophthora spp. that are important to the nursery industry. To address this, we conducted a series of experiments to evaluate how temperature affects the biology and control of three soilborne Phytophthora spp. prevalent in the nursery industry. In the first set of experiments, we evaluated the mycelial growth and sporulation of several Phytophthora cinnamomi, P. plurivora, and P. pini isolates at temperatures ranging from 4 to 42°C for different amounts of time (0 to 120 h). In the second set of experiments, we evaluated the response of three isolates of each species to the fungicides mefenoxam and phosphorous acid at temperatures ranging from 6 to 40°C. Results showed that each species responds differently to temperature, with P. plurivora having the greatest optimal temperature (26.6°C), P. pini the least (24.4°C), and P. cinnamomi was intermediate between the two (25.3°C). P. plurivora and P. pini had the lowest minimum temperatures (approximately 2.4°C) compared with P. cinnamomi (6.5°C), while all three species had a similar maximum temperature (approximately 35°C). When tested against mefenoxam, all three species were generally more sensitive to mefenoxam at cool temperatures (6 to 14°C) than at warmer temperatures (22 to 30°C). P. cinnamomi was also more sensitive to phosphorous acid at cool temperatures (6 to 14°C). However, both P. plurivora and P. pini tended to be more sensitive to phosphorous acid at warmer temperatures (22 to 30°C). These findings help define the temperatures at which these pathogens will be the most damaging and help delineate the temperatures at which fungicides should be applied for maximum efficacy.

A Metabolome Analysis and the Immunity of Phlomis purpurea against Phytophthora cinnamomi

Phlomis purpurea grows spontaneously in the southern Iberian Peninsula, namely in cork oak (Quercus suber) forests. In a previous transcriptome analysis, we reported on its immunity against Phytophthora cinnamomi. However, little is known about the involvement of secondary metabolites in the P. purpurea defense response. It is known, though, that root exudates are toxic to this pathogen. To understand the involvement of secondary metabolites in the defense of P. purpurea, a metabolome analysis was performed using the leaves and roots of plants challenged with the pathogen for over 72 h. The putatively identified compounds were constitutively produced. Alkaloids, fatty acids, flavonoids, glucosinolates, polyketides, prenol lipids, phenylpropanoids, sterols, and terpenoids were differentially produced in these leaves and roots along the experiment timescale. It must be emphasized that the constitutive production of taurine in leaves and its increase soon after challenging suggests its role in P. purpurea immunity against the stress imposed by the oomycete. The rapid increase in secondary metabolite production by this plant species accounts for a concerted action of multiple compounds and genes on the innate protection of Phlomis purpurea against Phytophthora cinnamomi. The combination of the metabolome with the transcriptome data previously disclosed confirms the mentioned innate immunity of this plant against a devastating pathogen. It suggests its potential as an antagonist in phytopathogens' biological control. Its application in green forestry/agriculture is therefore possible.

Pathogenicity and fungicide sensitivity of Phytophthora parvispora, a new pathogen causing gummosis and root rot disease on citrus trees

In 2021, pomelo (Citrus grandi) trees grown in Tuyen Quang and Phu Tho in northern Vietnam suffered from leaf yellowing, gummosis on stems, brown rot on fruit, and black rot on roots. Based on morphological and sequence analysis of the ITS and cox1 gene regions, the pathogen causing gummosis and root rot of citrus trees was identified as Phytophthora parvispora. Pathogenicity assays using mycelial plugs and zoospore suspension showed that P. parvispora induces disease symptoms on both the upper and lower parts of various citrus trees, including pomelo, orange (C. sinensis), and lime (C. aurantiifolia). This is the first report of P. parvispora as the causative agent of gummosis and root rot on various citrus trees in South-East Asia as well as in Vietnam. Further, P. parvispora was sensitive to all tested fungicides, including mancozeb, chlorothalonil, fosetyl aluminium, potassium phosphonate, and dimethomorph. These findings will have important implications for the effective management of gummosis and root rot disease of citrus trees.

Biocontrol and plant growth promoting traits of two avocado rhizobacteria are orchestrated by the emission of diffusible and volatile compounds

Avocado (Persea americana Mill.) is a tree crop of great social and economic importance. However, the crop productivity is hindered by fast-spreading diseases, which calls for the search of new biocontrol alternatives to mitigate the impact of avocado phytopathogens. Our objectives were to evaluate the antimicrobial activity of diffusible and volatile organic compounds (VOCs) produced by two avocado rhizobacteria (Bacillus A8a and HA) against phytopathogens Fusarium solani, Fusarium kuroshium, and Phytophthora cinnamomi, and assess their plant growth promoting effect in Arabidopsis thaliana. We found that, in vitro, VOCs emitted by both bacterial strains inhibited mycelial growth of the tested pathogens by at least 20%. Identification of bacterial VOCs by gas chromatography coupled to mass spectrometry (GC-MS) showed a predominance of ketones, alcohols and nitrogenous compounds, previously reported for their antimicrobial activity. Bacterial organic extracts obtained with ethyl acetate significantly reduced mycelial growth of F. solani, F. kuroshium, and P. cinnamomi, the highest inhibition being displayed by those from strain A8a (32, 77, and 100% inhibition, respectively). Tentative identifications carried out by liquid chromatography coupled to accurate mass spectrometry of diffusible metabolites in the bacterial extracts, evidenced the presence of some polyketides such as macrolactins and difficidin, hybrid peptides including bacillaene, and non-ribosomal peptides such as bacilysin, which have also been described in Bacillus spp. for antimicrobial activities. The plant growth regulator indole-3-acetic acid was also identified in the bacterial extracts. In vitro assays showed that VOCs from strain HA and diffusible compounds from strain A8a modified root development and increased fresh weight of A. thaliana. These compounds differentially activated several hormonal signaling pathways involved in development and defense responses in A. thaliana, such as auxin, jasmonic acid (JA) and salicylic acid (SA); genetic analyses suggested that developmental stimulation of the root system architecture by strain A8a was mediated by the auxin signaling pathway. Furthermore, both strains were able to enhance plant growth and decreased the symptoms of Fusarium wilt in A. thaliana when soil-inoculated. Collectively, our results evidence the potential of these two rhizobacterial strains and their metabolites as biocontrol agents of avocado pathogens and as biofertilizers.

Efficacy and Timing of Application of Fungicides, Biofungicides, Host-Plant Defense Inducers, and Fertilizer to Control Phytophthora Root Rot of Flowering Dogwood in Simulated Flooding Conditions in Container Production

Phytophthora root rot, caused by Phytophthora cinnamomi Rands, is one of the major diseases of flowering dogwood (Cornus florida L.). The severity of root rot disease increases when the plants are exposed to flooding conditions. A study was conducted to determine the efficacy and timing of application of different fungicides, biofungicides, host-plant defense inducers, and fertilizer to manage Phytophthora root rot in month-old seedlings in simulated flooding events for 1, 3, and 7 days. Preventative treatments were drench applied 3 weeks and 1 week before flooding whereas curative treatments were applied 24 h after flooding. Dogwood seedlings were inoculated with P. cinnamomi 3 days before the flooding. Plant height and width were recorded at the beginning and end of the study. At the end of the study, plant total weight and root weight were recorded and disease severity in the root was assessed using a scale of 0 to 100%. Root samples were plated using PARPH-V8 medium to determine the percent recovery of the pathogen. Empress Intrinsic, Pageant Intrinsic, Segovis, and Subdue MAXX, as preventative and curative applications, were able to suppress the disease severity compared with the inoculated control in all flooding durations. All treatments, with the exception of Stargus as a preventative application 3 weeks before flooding and Orkestra Intrinsic as a curative application, were able to suppress the disease severity compared with the inoculated control for a 1-day flooding event. Aliette and ON-Gard were effective in the first trial when applied preventatively at both 1 week and 3 weeks before flooding but not in the second trial. Signature Xtra was effective as a preventative application but not as a curative application. Interface was effective as a curative application but not as a preventative application. The findings of this study will help nursery growers to understand the performance of fungicides, biofungicides, host-plant defense inducers, and fertilizer at different time intervals and repeated applications to manage Phytophthora root rot in flooding conditions.

Comparative sub-cellular proteome analyses reveals metabolic differentiation and production of effector-like molecules in the dieback phytopathogen Phytophthora cinnamomi

Phytopathogenic oomycetes pose a significant threat to global biodiversity and food security. The proteomes of these oomycetes likely contain important factors that contribute to their pathogenic success, making their discovery crucial for elucidating pathogenicity. Phytophthora cinnamomi is a root pathogen that causes dieback in a wide variety of crops and native vegetation world-wide. Virulence proteins produced by P. cinnamomi are not well defined and a large-scale approach to understand the biochemistry of this pathogen has not been documented. Soluble mycelial, zoospore and secreted proteomes were obtained and label-free quantitative proteomics was used to compare the composition of the three sub-proteomes. A total of 4635 proteins were identified, validating 17.7% of the predicted gene set. The mycelia were abundant in transporters for nutrient acquisition, metabolism and cellular proliferation. The zoospores had less metabolic related ontologies but were abundant in energy generating, motility and signalling associated proteins. Virulence-associated proteins were identified in the secretome such as candidate effector and effector-like proteins, which interfere with the host immune system. These include hydrolases, cell wall degrading enzymes, putative necrosis-inducing proteins and elicitins. The secretome elicited a hypersensitive response on the roots of a model host and thus suggests evidence of effector activity. SIGNIFICANCE: Phytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and several horticultural crops such as avocado, pineapple and macadamia. Whilst this pathogen has significance world-wide, its pathogenicity and virulence have not been described in depth. We carried out comparative label-free proteomics of the mycelia, zoospores and secretome of P. cinnamomi. This study highlights the differential metabolism and cellular processes between the sub-proteomes. Proteins associated with metabolism, nutrient transport and cellular proliferation were over represented in the mycelia. The zoospores have a specialised proteome showing increased energy generation geared towards motility. Candidate effectors and effector-like secreted proteins were also identified, which can be exploited for genetic resistance. This demonstrates a better understanding of the biology and pathogenicity of P. cinnamomi infection that can subsequently be used to develop effective methods of disease management.

Inhibitory Effects of Phenazine Compounds and Volatile Organic Compounds Produced by Pseudomonas aurantiaca ST-TJ4 Against Phytophthora cinnamomi

Phytophthora cinnamomi is an important plant pathogen that is widely distributed worldwide and has caused serious ecological damage and significant economic losses in forests and plantations in many countries. The use of plant growth-promoting rhizobacteria is an effective and environmentally friendly strategy for controlling diseases caused by P. cinnamomi. In this study, we investigated the antagonistic mechanism of Pseudomonas aurantiaca ST-TJ4 against P. cinnamomi through different antagonistic approaches, observations of mycelial morphology, study of mycelial metabolism, and identification of antagonistic substances. The results showed that Pseudomonas aurantiaca ST-TJ4 was able to significantly inhibit mycelial growth, causing mycelial deformation and disrupting internal cell structures. Additionally, pathogen cell membranes were damaged by ST-TJ4, and mycelial cell content synthesis was disrupted. Ultraperformance liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry analyses showed that phenazine compounds and 2-undecanone were the main antagonistic components. The ammonia produced by the ST-TJ4 strain also contributed to the inhibition of the growth of P. cinnamomi. In conclusion, our results confirm that Pseudomonas aurantiaca ST-TJ4 can inhibit P. cinnamomi through multiple mechanisms and can be used as a biological control agent for various plant diseases caused by P. cinnamomi.

European and American chestnuts: An overview of the main threats and control efforts

Chestnuts are multipurpose trees significant for the economy and wildlife. These trees are currently found around the globe, demonstrating their genetic adaptation to different environmental conditions. Several biotic and abiotic stresses have challenged these species, contributing to the decline of European chestnut production and the functional extinction of the American chestnut. Several efforts started over the last century to understand the cellular, molecular, and genetic interactions behind all chestnut biotic and abiotic interactions. Most efforts have been toward breeding for the primary diseases, chestnut blight and ink disease caused by the pathogens, Cryphonectria parasitica and Phytophthora cinnamomi, respectively. In Europe and North America, researchers have been using the Asian chestnut species, which co-evolved with the pathogens, to introgress resistance genes into the susceptible species. Breeding woody trees has several limitations which can be mostly related to the long life cycles of these species and the big genome landscapes. Consequently, it takes decades to improve traits of interest, such as resistance to pathogens. Currently, the availability of genome sequences and next-generation sequencing techniques may provide new tools to help overcome most of the problems tree breeding is still facing. This review summarizes European and American chestnut's main biotic stresses and discusses breeding and biotechnological efforts developed over the last decades, having ink disease and chestnut blight as the main focus. Climate change is a rising concern, and in this context, the adaptation of chestnuts to adverse environmental conditions is of extreme importance for chestnut production. Therefore, we also discuss the abiotic challenges on European chestnuts, where the response to abiotic stress at the genetic and molecular level has been explored.

A Review of the Stress Resistance, Molecular Breeding, Health Benefits, Potential Food Products, and Ecological Value of Castanea mollissima

Chestnut (Castanea spp., Fagaceae family) is an economically and ecologically valuable species. The main goals of chestnut production vary among species and countries and depend on the ecological characteristics of orchards, agronomic management, and the architecture of chestnut trees. Here, we review recent research on chestnut trees, including the effects of fungal diseases (Cryphonectria parasitica and Phytophthora cinnamomi) and insect pests (Dryocosmus kuriphilus Yasumatsu), molecular markers for breeding, ecological effects, endophytic fungi, and extracts with human health benefits. We also review research on chestnut in the food science field, technological improvements, the soil and fertilizer used for chestnut production, and the postharvest biology of chestnut. We noted differences in the factors affecting chestnut production among regions, including China, the Americas, and Europe, especially in the causal agents of disease and pests. For example, there is a major difference in the resistance of chestnut to C. parasitica in Asian, European, and American countries. Our review provides new insights into the integrated disease and pest management of chestnut trees in China. We hope that this review will foster collaboration among regions and help to clarify differences in the direction of breeding efforts among countries.

Population Genetic Analyses of Phytophthora cinnamomi Reveals Three Lineages and Movement Between Natural Vegetation and Avocado Orchards in South Africa

Phytophthora cinnamomi is the causal agent of root rot, canker, and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses to forestry and agricultural industries, but also threatens the health of various plants in natural ecosystems. In this study, 380 isolates of P. cinnamomi from four avocado production areas and two regions of natural vegetation in South Africa were investigated using 15 microsatellite markers. These populations were found to have a low level of genetic diversity and consisted of isolates from three lineages. Shared genotypes were detected between isolates from avocado orchards and natural vegetation, indicating the movement of isolates between these areas. The population from the Western Cape natural vegetation had the highest level of genotypic diversity and number of unique alleles, indicating this could be the point of introduction of P. cinnamomi to South Africa. Index of association analysis suggested that five of six populations were under linkage disequilibrium, suggesting a clonal mode of reproduction, whereas genotypes sampled from a recently established avocado orchard in the Western Cape were derived from a randomly recombining population. This study provided novel insights on the genetic diversity and spread of P. cinnamomi in South Africa. It also reported on the predominance of triploidy in natural occurring populations and provided evidence for recombination of P. cinnamomi for the first time. The presence of two dominant genotypes in all avocado production areas in South Africa highlight the importance of considering them in disease management and resistance breeding programs.

Relationship of alien species continues in a foreign land: The case of Phytophthora and Australian Banksia (Proteaceae) in South African Fynbos

Fungal invasions only recently started to receive more attention in invasion biology. This is largely attributed to little or non‐existent information about these inconspicuous organisms. Most invasion hypotheses focus on factors that increase invasion success; few try to explain why invasions fail. Here we hypothesize that a host–pathogen relationships can limit the invasiveness of an alien plant species in a novel range. To test this, we investigate whether the invasiveness of the Australian genus of Proteaceae, Banksia, in South Africa is determined by the alien and major invasive phytopathogen, Phytophthora cinnamomi. The presence of P. cinnamomi in Banksia root and soil was evaluated using morphological and molecular techniques. Isolates were cultured onto selective media and polymerize chain reactions and internal transcribing spacers were used for identification. Acetone leaf extracts of 11 Banksia spp. were screened for antimicrobial activity against P. cinnamomi, using the minimum inhibitory concentration assay. A total of 3840 Banksia individuals from seven localities were surveyed. Phytophthora  cinnamomi was consistently isolated from Banksia species root and soil samples. Out of the 12 Banksia species that were screened for antimicrobial activity, four introduced species, B. burdettii, B. coccinea, Banksia hookeriana, and B. prionotes and the invasive B. integrifolia and B. ericifolia exhibited relatively high antimicrobial activity against P. cinnamomi (strain 696/12). We show that the phytopathogen in the native range has similar impact in the novel range and in doing so may limit invasion success of Banksia species with low antimicrobial activity.

Differing Responses to Phytophthora cinnamomi Infection in Susceptible and Partially Resistant Persea americana (Mill.) Rootstocks: A Case for the Role of Receptor-Like Kinases and Apoplastic Proteases

The hemibiotrophic plant pathogen Phytophthora cinnamomi Rands is the most devastating pathogen of avocado (Persea americana Mill.) and, as such, causes significant annual losses in the industry. Although the molecular basis of P. cinnamomi resistance in avocado and P. cinnamomi virulence determinants have been the subject of recent research, none have yet attempted to compare the transcriptomic responses of both pathogen and host during their interaction. In the current study, the transcriptomes of both avocado and P. cinnamomi were explored by dual RNA sequencing. The basis for partial resistance was sought by the inclusion of both susceptible (R0.12) and partially resistant (Dusa®) rootstocks sampled at early (6, 12 and 24 hours post-inoculation, hpi) and late time-points (120 hpi). Substantial differences were noted in the number of differentially expressed genes found in Dusa® and R0.12, specifically at 12 and 24 hpi. Here, the partially resistant rootstock perpetuated defense responses initiated at 6 hpi, while the susceptible rootstock abruptly reversed course. Instead, gene ontology enrichment confirmed that R0.12 activated pathways related to growth and development, essentially rendering its response at 12 and 24 hpi no different from that of the mock-inoculated controls. As expected, several classes of P. cinnamomi effector genes were differentially expressed in both Dusa® and R0.12. However, their expression differed between rootstocks, indicating that P. cinnamomi might alter the expression of its effector arsenal based on the rootstock. Based on some of the observed differences, several P. cinnamomi effectors were highlighted as potential candidates for further research. Similarly, the receptor-like kinase (RLK) and apoplastic protease coding genes in avocado were investigated, focusing on their potential role in differing rootstock responses. This study suggests that the basis of partial resistance in Dusa® is predicated on its ability to respond appropriately during the early stages following P. cinnamomi inoculation, and that important components of the first line of inducible defense, apoplastic proteases and RLKs, are likely to be important to the observed outcome.

Phytophthora cinnamomi causing root rot on Rhododendron lapponicum and control it using potential biocontrol agents

Rhododendron lapponicum (R. lapponicum) is a dwarf Rhododendron species, which is severely infected with root rot and wilt in Yunnan province, China. However, the causal agent causing these symptoms was unknown. An isolate, Pci-1 was identified as Phytophthora cinnamomi, based on its morphology and the sequences of β-tubulin, internal transcribed spacer, and Ypt1 genes and verified according to the Koch's postulate. We found that this pathogen could infect 14 species of plants, including Althaea rosea, Viburnum cylindricum, and Brassica napus. Strain Pci-1 could cause R. lapponicum to wither and die; and it grows best in an oat medium with pH 7.0 - 8.0 and an optimum temperature of 27°C. We suggest that the rhizosphere of R. lapponicum treated with biocontrol strains Paenibacillus polymyxoides P2-5 and Trichoderma asperellum Tv-1 showed a significant inhibitory effect on pathogen Pci-1. The inhibitory effect of 70% dimethomorph + cymoxanil was significantly higher with EC₅₀ and EC₉₀ values of 0.1894 and 0.3618 a.i. µg/ml, respectively. Greenhouse experiments revealed that the pathogen load is decreased in the presence of potential antagonists. This study provides fundamentals on risk assessment and theoretical support for the management of P. cinnamomi pathogen and contributes significantly to the planting of forest and horticultural crops in a disease-free environment.

Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis

The B. safensis RGM 2450 and B. siamensis RGM 2529 strains were isolated from the rhizosphere of plants presenting resilience to abiotic and biotic stress conditions. To understand the implications of bacteria in resilience, a genomic and experimental analysis was carried out on their biostimulant and phytopathogenic antagonist properties. Genome analyses of both strains indicated that they have the potential to synthesize bioactive compounds such as the battery of non-ribosomal peptides, polyketides, extracellular enzymes and phytohormones. These results were consistent with the antagonistic activities of both strains against the phytopathogens Botrytis cinerea, Colletotrichum acutatum, Fusarium oxysporum and Phytophtora cinnamomi. They also showed the capacity to solubilize phosphorus, fix nitrogen and produce indole acetic acid. This was observed in tomato seedlings grown from seeds inoculated with the mixture of strains which presented significantly greater length as well as wet and dry weight in comparison with the treatments individually inoculated with each strain and the control. Accordingly, the combination of B. safensis RGM 2450 and B. siamensis RGM 2529 showed synergistic biostimulant activity. These findings contribute new knowledge of the genomic and metabolomic properties taking part in the symbiotic interactions between these strains and the plants and uphold the combined use of both strains as a biostimulant.

Management of Phytophthora cinnamomi Using Fungicides and Host Plant Defense Inducers Under Drought Conditions: A Case Study of Flowering Dogwood

Phytophthora cinnamomi is considered one of the most destructive pathogens of ornamental crops. Different fungicides and host plant defense inducers were tested for their efficacy in managing Phytophthora root rot in drought conditions. In this study, the drought conditions were maintained by evaluating the moisture-holding capacity of the pine bark in a 10.2-cm nursery container. Four controls and nine different treatments were used in two trials for this greenhouse study. All treatments were drench-applied as a preventative or curative treatment. Seedlings were artificially inoculated with P. cinnamomi. Regular irrigation was carried out using overhead irrigation for 1 month after inoculation. Irrigation was regulated by drip irrigation after the first month. A moisture level of 15% to 18% of total moisture-holding capacity was maintained using the gravimetric method throughout the drought period. Physiological parameters of the seedlings were recorded a week after seedlings were drought stressed. In both trials of preventative and curative treatments, all treatments were able to suppress the disease significantly except Orkestra Intrinsic. Orkestra Intrinsic had a disease severity statistically similar to the inoculated and stressed control in trial 1 of the curative treatment. Net photosynthesis, stomatal conductance, and leaf moisture potential were significantly greater in seedlings treated with Subdue MAXX, Signature Xtra, and Empress Intrinsic in both trials of preventative and curative treatments. Effective quantum yield of Photosystem II was significantly lower in the inoculated stressed control in both trials of preventative and curative treatments. Net chlorophyll content through the SPAD meter showed higher values for Subdue MAXX treated seedlings compared with the noninoculated nonstressed controls in trial 1 as both a curative and preventative application. In trial 2, Subdue MAXX and Signature Xtra were the best curative treatments, whereas Empress Intrinsic, Interface, and Subdue MAXX were the best preventative treatments for higher chlorophyll content. This case study will help growers perform successful management of Phytophthora root rot in woody ornamental crops during drought or water deficit conditions.

Seaweed Extract-Stimulated Priming in Arabidopsis thaliana and Solanum lycopersicum

Plant priming is an induced physiological state where plants are protected from biotic and abiotic stresses. Whether seaweed extracts promote priming is largely unknown as is the mechanism by which priming may occur. In this study, we examined the effect of a seaweed extract (SWE) on two distinct stages of plant priming (priming phase and post-challenge primed state) by characterising (i) plant gene expression responses using qRT-PCR and (ii) signal transduction responses by evaluating reactive oxygen species (ROS) production. The SWE is made from the brown algae Ascophyllum nodosum and Durvillaea potatorum. The priming phase was examined using both Arabidopsis thaliana and Solanum lycopersicum. At this stage, the SWE up-regulated key priming-related genes, such as those related to systemic acquired resistance (SAR) and activated the production of ROS. These responses were found to be temporal (lasting 3 days). The post-challenge primed state was examined using A. thaliana challenged with a root pathogen. Similarly, defence response-related genes, such as PR1 and NPR1, were up-regulated and ROS production was activated (lasting 5 days). This study found that SWE induces plant priming-like responses by (i) up-regulating genes associated with plant defence responses and (ii) increasing production of ROS associated with signalling responses.

In silico characterization of molecular factors involved in metabolism and pathogenicity of Phytophthora cinnamomi

Phytophthora cinnamomi is classified as one of the most devastating plant pathogens in the world. It has a destructive effect on more than 5000 horticultural and forestry species in the world, and especially on Castanea sativa. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus like organisms which provoke plant diseases via motile zoospores. Control of this organism is considered very challenging because of the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires in-depth knowledge of the cellular and molecular bases of development and metabolism. The aim of this review was to identify molecular factors associated with the metabolism of P. cinnamomi by studying the genes implicated in fundamental metabolism using tools of bioinformatics. Also, some genes involved in pathogenicity will be cited and characterized, such as genes coding for transglycosylases. Genomic sequences of P. cinnamomi were analyzed using an open reading frame (ORF) finder. The identified ORFs products (proteins) were compared to sequences already described and with known functions present in databases such as NCBI and fungi database. In this way, homologous proteins were found, with the respective specific domains, to proteins involved in the metabolism and pathogenicity of Phytophthora ssp.

Optimizing Inoculum Production Methods for Infesting Soil with Phytophthora Species

Inoculum production is an important part of conducting research with soilborne Phytophthora species. One common method is to incubate Phytophthora cultures in nutrient-amended vermiculite. However, inoculum levels often vary among batches of inoculum, even when production methods remain the same, and incubation typically takes ≥6 weeks, increasing risks for delayed experiments if the resulting inoculum level is too low. A more reliable and rapid method is needed for future studies. Experiments were conducted to determine inoculum levels of Phytophthora cinnamomi and Phytophthora plurivora after incubation in V8 juice-amended vermiculite (standard method); evaluate how inoculum viability was affected by air-drying; develop a modified method that takes less time to produce a vermiculite-based inoculum; and evaluate the effect of storage on inoculum viability. Results showed that the standard method produced inoculum levels from 716 to 1,808 colony forming units (CFUs)/g and that drying to <78% moisture content significantly reduced viability. The modified method used 2-week-old Phytophthora cultures to infest vermiculite at 80% moisture content and produced inoculum levels from 214 to 525 CFU/g. Storage for >1 day generally reduced inoculum viability. Although inoculum levels from the modified method were lower than the standard method, inoculum levels for each isolate were more consistent between trials, and the modified method was 6 to 8 weeks faster. Production with the modified method can also be easily scaled up by infesting a greater volume of vermiculite with additional cultures of Phytophthora. These results are important because they help explain variability in soilborne Phytophthora inoculum production and storage and provide a new method for producing inoculum more quickly.

Identification and Characterization of Arbutus unedo L. Endophytic Bacteria Isolated from Wild and Cultivated Trees for the Biological Control of Phytophthora cinnamomi

Arbutus unedo L. is a resilient tree with a circum-Mediterranean distribution. Besides its ecological relevance, it is vital for local economies as a fruit tree. Several microorganisms are responsible for strawberry tree diseases, leading to production constrictions. Thus, the development of alternative plant protection strategies is necessary, such as bacterial endophytes, which may increase their host’s overall fitness and productivity. As agricultural practices are a driving factor of microbiota, this paper aimed to isolate, identify and characterize endophytic bacteria from strawberry tree leaves from plants growing spontaneously in a natural environment as well as from plants growing in orchards. A total of 62 endophytes were isolated from leaves and identified as Bacillus, Paenibacillus, Pseudomonas, Sphingomonas and Staphylococcus. Although a slightly higher number of species was found in wild plants, no differences in terms of diversity indexes were found. Sixteen isolates were tested in vitro for their antagonistic effect against A. unedo mycopathogens. B. cereus was the most effective antagonist causing a growth reduction of 20% in Glomerella cingulata and 40% in Phytophthora cinnamomi and Mycosphaerella aurantia. Several endophytic isolates also exhibited plant growth-promoting potential. This study provides insights into the diversity of endophytic bacteria in A. unedo leaves and their potential role as growth promoters and pathogen antagonists.

Disentangling the role of oomycete soil pathogens as drivers of plant-soil feedbacks

Interactions among plant species and their soil biota drive plant-soil feedbacks (PSFs) that play a major role in the dynamics and diversity of plant communities. Among the different components of the soil community, pathogens are considered to be the main drivers of negative PSFs. Despite this, the number of studies that have experimentally quantified the contribution of soil pathogens to PSFs remains considerably low. Here we conducted a greenhouse experiment with oomycete-specific fungicide to quantify the contribution of soil pathogens, and particularly oomycete pathogens, to individual and pairwise PSFs in forest communities. We used as a case study Mediterranean mixed forests dominated by Quercus suber and invaded by the oomycete pathogen Phytophthora cinnamomi. The fungicide treatment was crossed with a competition treatment to explore how conspecific neighbors might modify pathogen effects. To place the results of the experiment in a wider context, we also conducted a systematic review of published papers that explicitly used fungicide to explore the role of pathogens in PSF experiments. Our experimental results showed that oomycete pathogens were the main drivers of individual PSFs in the study forests. Oomycete effects varied among tree species according to their susceptibility to P. cinnamomi, driving negative PSFs in the highly susceptible Q. suber but not in the coexistent Olea europaea. Oomycete-driven PSFs were not modified by intraspecific competition. Oomycete pathogens were also major contributors to negative pairwise PSFs assumed to promote species coexistence. Results from the systematic review supported the novelty of our experimental results, since only three studies had previously used oomycete-specific fungicide in a PSF context and none in systems invaded by exotic oomycetes. Overall, our results provide novel evidence of oomycete pathogens (including the exotic P. cinnamomi) as fundamental drivers of negative individual and pairwise PSFs with implications for species coexistence in invaded communities. Although in the short-term invasive pathogens might contribute to species coexistence by causing self-limitation in dominant species, strong inter-specific variation in self-limitation might undermine coexistence in the long-term. Because of the increasing number of exotic oomycetes worldwide, further attention should be given to oomycetes as drivers of PSFs in plant communities.

Modelling affected regions by the Iberian Quercus disease with proximity diagrams

In this work, we propose a mathematical model to determine the potential propagation areas of the Mediterranean Quercus disease commonly referred to as "seca" (Tuser and Sánchez 2004) in specific areas of Extremadura. Although it is a syndrome of complex etiology caused by the action of the different biotic (insects and fungi) and abiotic factors (temperature, orography, soil, etc.), numerous studies suggest that the soil-borne pathogen cinnamomi represents the main responsible for the decay of the holm and cork oak. However, very little is known about the Phytophthora epidemic distribution patterns and its geographical dependence on other factors that favor its spread. With the aim to clarify this question, in this paper, we will use optimal computational geometry algorithms based on proximity diagrams that allow us to design a pathogen transmission map and to determine its correlation with different causing agents, specially with the presence of standing water or drainage lines water.

Susceptibility of Garden Plants to Phytophthora Root Rot

Phytophthora root rot (PRR) is a serious disease of horticultural, forest, and ornamental plant species caused by species of the oomycete genus Phytophthora. Their wide host range makes the choice of resistant plants in the management of the disease difficult. We used the Royal Horticultural Society diagnostic dataset of PRR records from U.K. gardens to compare the susceptibility of different host genera to the disease. The dataset was compared with existing reports of plants recorded as notably resistant or notably susceptible to PRR. An index-based approach was used to separate 177 genera of woody plants into three categories: 85 were low index (<0.10: rarely affected), 34 were medium index (0.10 to 0.20: sometimes affected) and 58 were high index (>0.20: frequently affected). Similarly, genera of nonwoody plants were separated into: 45 low index (<0.22), 16 medium index (0.22 to 0.44), and 18 high index (>0.44). Taxus was the genus with the highest index, while most genera in the Malvales and Ericales were in the high-index group. Most genera in the Myrtales, Fabales, and Monocotyledons were low index. While 30 Phytophthora species were recorded in our study, the wide host range spp., P. plurivora, P. cryptogea, and P. cinnamomi, represented 63% of identifications. P. plurivora was the most common species on woody plants and P. cryptogea on nonwoody plants. These results provide confidence in the use of host resistance as part of the integrated management of PRR.

Identification of Susceptibility Genes in Castanea sativa and Their Transcription Dynamics following Pathogen Infection

Castanea sativa is one of the main multipurpose tree species valued for its timber and nuts. This species is susceptible to two major diseases, ink disease and chestnut blight, caused by Phytophthora spp. and Cryphonectria parasitica, respectively. The loss-of-function mutations of genes required for the onset of pathogenesis, referred to as plant susceptibility (S) genes, are one mechanism of plant resistance against pathogens. On the basis of sequence homology, functional domain identification, and phylogenetic analyses, we report for the first time on the identification of S-genes (mlo1, dmr6, dnd1, and pmr4) in the Castanea genus. The expression dynamics of S-genes were assessed in C. sativa and C. crenata plants inoculated with P. cinnamomi and C. parasitica. Our results highlighted the upregulation of pmr4 and dmr6 in response to pathogen infection. Pmr4 was strongly expressed at early infection phases of both pathogens in C. sativa, whereas in C. crenata, no significant upregulation was observed. The infection of P. cinnamomi led to a higher increase in the transcript level of dmr6 in C. sativa compared to C. crenata-infected samples. For a better understanding of plant responses, the transcript levels of defense genes gluB and chi3 were also analyzed.

Phytophthora Species Differ in Response to Phosphorous Acid and Mefenoxam for the Management of Phytophthora Root Rot in Rhododendron

Phytophthora root rot, caused by many soilborne Phytophthora spp., is a significant disease affecting the $42 million rhododendron nursery industry. Rhododendron growers have increasingly reported failure by two systemic fungicides, phosphorous acid and mefenoxam, to adequately control root rot. Both fungicides may be applied as a foliar spray or soil drench but it is unknown how application method, fungicide chemistry, or pathogen diversity affects disease control. Therefore, two experiments were conducted to (i) determine whether differences in application method or fungicide chemistry affect control of root rot caused by P. cinnamomi and P. plurivora and (ii) evaluate the sensitivity of Phytophthora spp. and isolates from the rhododendron industry to each fungicide. Results demonstrated that soil drenches of either fungicide were more effective than foliar sprays for control of P. cinnamomi but were ineffective for P. plurivora. Furthermore, Phytophthora spp. and isolates varied in sensitivity to phosphorous acid and mefenoxam, and there were multiple fungicide-insensitive isolates, especially within P. plurivora. Differences in sensitivity were also observed among isolates from different nurseries and production systems, with some nurseries having less sensitive isolates than others and with container systems generally having less sensitive isolates than field systems. Our results provide three potential reasons for why fungicide control of Phytophthora root rot might fail: (i) the fungicide can be applied to the wrong portion of the plant for optimal control, (ii) there are differences in fungicide sensitivity among soilborne Phytophthora spp. and isolates infecting rhododendron, and (iii) fungicide-insensitive isolates are present in the rhododendron nursery industry.

Screening a Natural Product-Inspired Library for Anti-Phytophthora Activities

Phytophthora is a genus of microorganisms that cause devastating dieback and root-rot diseases in thousands of plant hosts worldwide. The economic impact of Phytophthora diseases on crops and native ecosystems is estimated to be billions of dollars per annum. These invasive pathogens are extremely difficult to control using existing chemical means, and the effectiveness of the few treatments available is being jeopardized by increasing rates of resistance. There is an urgent need to identify new chemical treatments that are effective against Phytophthora diseases. Natural products have long been regarded as "Nature's medicine chest", providing invaluable leads for developing front-line drugs and agrochemical agents. Here, we have screened a natural product-inspired library of 328 chemicals against two key Phytophthora species: Phytophthora cinnamomi and Phytophthora agathidicida. The library was initially screened for inhibition of zoospore germination. From these screens, we identified twenty-one hits that inhibited germination of one or both species. These hits were further tested in mycelial growth inhibition studies to determine their half-maximal inhibitory concentrations (IC₅₀s). Four compounds had IC₅₀ values of approximately 10 µM or less, and our best hit had IC₅₀s of approximately 3 µM against both Phytophthora species tested. Overall, these hits may serve as promising leads for the development of new anti-Phytophthora agrochemicals.

Expression of Castanea crenata Allene Oxide Synthase in Arabidopsis Improves the Defense to Phytophthora cinnamomi

Allene oxide synthase (AOS) is a key enzyme of the jasmonic acid (JA) signaling pathway. The AOS gene was previously found to be upregulated in an Asian chestnut species resistant to infection by the oomycete Phytophthora cinnamomi (Castanea crenata), while lower expression values were detected in the susceptible European chestnut (Castanea sativa). Here, we report a genetic and functional characterization of the C. crenata AOS (CcAOS) upon its heterologous gene expression in a susceptible ecotype of Arabidopsis thaliana, which contains a single AOS gene. It was found that Arabidopsis plants expressing CcAOS delay pathogen progression and exhibit more vigorous growth in its presence. They also show upregulation of jasmonic acid and salicylic acid-related genes. As in its native species, heterologous CcAOS localized to plastids, as revealed by confocal imaging of the CcAOS-eGFP fusion protein in transgenic Arabidopsis roots. This observation was confirmed upon transient expression in Nicotiana benthamiana leaf epidermal cells. To further confirm a specific role of CcAOS in the defense mechanism against the pathogen, we performed crosses between transgenic CcAOS plants and an infertile Arabidopsis AOS knockout mutant line. It was found that plants expressing CcAOS exhibit normal growth, remain infertile but are significantly more tolerant to the pathogen than wild type plants. Together, our results indicate that CcAOS is an important player in plant defense responses against oomycete infection and that its expression in susceptible varieties may be a valuable tool to mitigate biotic stress responses.

Integrated Proteomic and Metabolomic Profiling of Phytophthora cinnamomi Attack on Sweet Chestnut (Castanea sativa) Reveals Distinct Molecular Reprogramming Proximal to the Infection Site and Away from It

Phytophthora cinnamomi is one of the most invasive tree pathogens that devastates wild and cultivated forests. Due to its wide host range, knowledge of the infection process at the molecular level is lacking for most of its tree hosts. To expand the repertoire of studied Phytophthora-woody plant interactions and identify molecular mechanisms that can facilitate discovery of novel ways to control its spread and damaging effects, we focused on the interaction between P. cinnamomi and sweet chestnut (Castanea sativa), an economically important tree for the wood processing industry. By using a combination of proteomics, metabolomics, and targeted hormonal analysis, we mapped the effects of P. cinnamomi attack on stem tissues immediately bordering the infection site and away from it. P. cinnamomi led to a massive reprogramming of the chestnut proteome and accumulation of the stress-related hormones salicylic acid (SA) and jasmonic acid (JA), indicating that stem inoculation can be used as an easily accessible model system to identify novel molecular players in P. cinnamomi pathogenicity.

The soil biotic community protects Rhododendron spp. across multiple clades from the oomycete Phytophthora cinnamomi at a cost to plant growth

The effects of whole soil biotic communities on plants is a result of positive and negative interactions from a complex suite of mutualists and pathogens. However, few experiments have evaluated the composite effects of whole soil biotic communities on plant growth and disease resistance. We conducted a factorial greenhouse experiment with 14 Rhododendron species grown with and without live conspecific soil biota and with and without the disease, Phytophthora cinnamomi. We tested the prediction that the presence of whole soil biotic communities influences survival in the presence of disease. We also explored functional trait correlations with disease susceptibility across the phylogeny. The presence of live soil biota led to higher survival in the presence of disease compared with sterilized soils, and the direction of this effect was consistent for seven species across four clades. The presence of live soil biota also significantly reduced plant growth rate and decreased shoot biomass, relative to plants grown in sterilized soil, indicating that live soil biota might influence plant allocation strategies. We found that Rhododendron species with higher Root Shoot Ratios were less susceptible to Phytophthora, suggesting that water relations influence disease susceptibility. Our findings that disease resistance and susceptibility occur independently across multiple clades and that whole soil biotic communities consistently enhance disease resistance across clades, suggest that soil biota may play an important role in disease resistance and can moderate disease-induced mortality.

Phaeophyceaean (Brown Algal) Extracts Activate Plant Defense Systems in Arabidopsis thaliana Challenged With Phytophthora cinnamomi

Seaweed extracts are important sources of plant biostimulants that boost agricultural productivity to meet current world demand. The ability of seaweed extracts based on either of the Phaeophyceaean species Ascophyllum nodosum or Durvillaea potatorum to enhance plant growth or suppress plant disease have recently been shown. However, very limited information is available on the mechanisms of suppression of plant disease by such extracts. In addition, there is no information on the ability of a combination of extracts from A. nodosum and D. potatorum to suppress a plant pathogen or to induce plant defense. The present study has explored the transcriptome, using RNA-seq, of Arabidopsis thaliana following treatment with extracts from the two species, or a mixture of both, prior to inoculation with the root pathogen Phytophthora cinnamomi. Following inoculation, five time points (0-24 h post-inoculation) that represented early stages in the interaction of the pathogen with its host were assessed for each treatment and compared with their respective water controls. Wide scale transcriptome reprogramming occurred predominantly related to phytohormone biosynthesis and signaling, changes in metabolic processes and cell wall biosynthesis, there was a broad induction of proteolysis pathways, a respiratory burst and numerous defense-related responses were induced. The induction by each seaweed extract of defense-related genes coincident with the time of inoculation showed that the plants were primed for defense prior to infection. Each seaweed extract acted differently in inducing plant defense-related genes. However, major systemic acquired resistance (SAR)-related genes as well as salicylic acid-regulated marker genes (PR1, PR5, and NPR1) and auxin associated genes were found to be commonly up-regulated compared with the controls following treatment with each seaweed extract. Moreover, each seaweed extract suppressed P. cinnamomi growth within the roots of inoculated A. thaliana by the early induction of defense pathways and likely through ROS-based signaling pathways that were linked to production of ROS. Collectively, the RNA-seq transcriptome analysis revealed the induction by seaweed extracts of suites of genes that are associated with direct or indirect plant defense in addition to responses that require cellular energy to maintain plant growth during biotic stress.

A Comparison of Immediate and Short-Term Defensive Responses to Phytophthora Species Infection in Both Susceptible and Resistant Walnut Rootstocks

Clonal rootstocks are one alternative used by the walnut industry to control damage caused by Phytophthora species, traditionally using plants grafted on susceptible Juglans regia rootstock. Vlach, VX211, and RX1 are clonal rootstocks with a degree of resistance to Phytophthora species. The resistance to pathogens in these rootstocks depends on the resistance mechanisms activated by the presence of the pathogen and subsequent development of responses in the host. In this work, we analyzed how plants of J. regia, Vlach, VX211, and RX1 responded to inoculation with Phytophthora cinnamomi or Phytophthora citrophthora isolates obtained from diseased English walnut plants from Chilean orchards. After inoculation, plants of Vlach, VX211, and RX1 showed canopy and root damage indexes that did not differ from noninoculated control plants. In contrast, plants of J. regia, which is susceptible to P. cinnamomi and P. citrophthora, died after inoculation. Vlach, VX211, and RX1 plants inoculated with P. cinnamomi or P. citrophthora showed greater root weight and volume and greater root growth rates than their respective controls. These results suggest that short-term carbohydrate dynamics may be related to the defense mechanisms of plants; they are immediately activated after inoculation through the production of phenolic compounds, which support the further growth and development of roots in walnut clonal rootstocks. To our knowledge, this is the first study that comprehensively characterizes vegetative and radicular growth and the dynamics of sugars and phenols in response to infection with P. cinnamomi or P. citrophthora in walnut rootstocks.

Synthesis and In Vitro Growth Inhibition of 2-Allylphenol Derivatives Against Phythopthora cinnamomi Rands

Phytophthora cinnamomi is a phytopathogen that causes extensive damage in different crops, and therefore, produces important economic losses all around the world. Chemical fungicides are a key factor for the control of this disease. However, ecological and environmental considerations, as well as the appearance of strains that are resistant to commercial fungicides, have prompted the quest for new antifungal agents which are of low ecological impact. In this work, a series of new 2-allylphenol derivatives was synthesized, and their structures were confirmed by FT-IR, NMR, and MS. Some of the synthesized compounds, more specifically nitro derivatives, exhibit strong growth inhibition of P. cinnamomi with EC₅₀ as low as 10.0 µg/mL. This level of activity is similar to that exhibited by METALAXYL MZ 58 WP, a commonly-used commercial fungicide; therefore, these compounds might be of agricultural interest due to their potential use as fungicides against P. cinnamomi. The results indicate that this activity depends on the chemical structures of the 2-allylphenol derivatives, and that it is strongly enhanced in molecules where nitro and hydroxyl groups adopt a -para configuration. These effects are discussed in terms of the electronic distribution of the aromatic ring induced by substituent groups.

Cloning and expression analysis of an endo-1,3-β-D-glucosidase from Phytophthora cinnamomi

Phytophthora is considered one of the most destructive genus for many agricultural plant species worldwide, with a strong environmental and economic impact. Phytophthora cinnamomi is a highly aggressive Phytophthora species associated with the forest decline and responsible for the ink disease in chestnut trees (Castanea sativa Miller), a culture which is extremely important in Europe. This pathogenicity occurs due to the action of several enzymes like the hydrolysis of 1,3-β-glucans at specific sites by the enzyme endo-1,3-β-D-glucosidase. The aim of this work to analyze the heterologous expression in two microorganisms, Escherichia coli and Pichia pastoris, of an endo-1,3-β-D-glucosidase encoded by the gene ENDO1 (AM259651) from P. cinnamomi. Different plasmids were used to clone the gene on each organism and the real-time quantitative polymerase chain reaction was used to determine its level of expression. Homologous expression was also analyzed during growth in different carbon sources (glucose, cellulose, and sawdust) and time-course experiments were used for endo-1,3-β-D-glucosidase production. The highest expression of the endo-1,3-β-D-glucosidase gene occurred in glucose after 8 h of induction. In vivo infection of C. sativa by P. cinnamomi revealed an increase in endo-1,3-β-D-glucosidase expression after 12 h. At 24 h its expression decreased and at 48 h there was again a slight increase in expression, and more experiments in order to further explain this fact are underway.

Spatio-temporal analysis of oak decline process in open woodlands: A case study in SW Spain

This study aims to characterize at landscape level the spatio-temporal dynamics of a massive oak decline that is occurring in dehesas ecosystems. We are looking at possibilities of matching with Phytophthora disease behavior, a harmful disease detected in the studied area, in order to interpret its implications within the context of the disease management. Spatial locations of affected trees from 2001, 2009 and 2016 identified through photointerpretation were analyzed with the inhomogeneous Ripley's K-function to assess their spatial pattern. Multivariate Adaptive Regression Splines (MARS), a non-parametric data mining method, was used to investigate the influence of a range of landscape descriptors of different nature on the proneness to oak decline, using the location of affected trees in comparison with that of healthy spots (points randomly extracted from areas covered by healthy trees). Affected trees showed a strong clustering pattern that decreased over time. The reported spatial patterns align with the hypothesis of Phytophthora cinnamomi Rands. being the main cause of oak decline in Mediterranean forests. Location of affected trees detected in different years was found to be spatially related, suggesting the implication of a contagion process. MARS models from 2001, 2009 and 2016 reported Area Under the Curve (AUC) values of 0.707, 0.671 and 0.651, respectively. Slope was the most influential landscape descriptor across the three years, with distance to afforestations being the second for 2001 and 2009. Landscape descriptors linked to human factors and soil water content seem to influence oak decline caused by Phytophthora cinnamomi at landscape level. Afforestations carried out as part of the afforestation subsidy program promoted by the European Commission in 1992 could have acted as an initial source of Phytophthora cinnamomi infection. These findings together with the consideration of the spatial and temporal scale of the spreading are essential when planning the management of oak decline in open woodlands.

Cloning, characterization, in vitro and in planta expression of a necrosis-inducing Phytophthora protein 1 gene npp1 from Phytophthora cinnamomi

The soil-borne oomycete Phytophthora cinnamomi is a highly destructive Phytophthora species associated with the decline of forest. This pathogen secretes a novel class of necrosis-inducing proteins known as Nep1-like proteins (NLPs). In this work, we report the sequencing and molecular characterization of one of these proteins, more specifically the necrosis-inducing Phytophthora protein 1 (NPP1). The ORF of the npp1 gene (EMBL database AM403130) has 768 bp encoding a putative peptide of 256 amino acids with a molecular weight of approximately 25 kD. In order to understand its function, in vitro gene expression was studied during growth in different carbon sources (glucose, cellulose, and sawdust), and at different times of infection, in vivo by RT-qPCR. The highest expression of the npp1 gene occurred in glucose medium followed by sawdust. In vivo infection of Castanea sativa roots with P. cinnamomi revealed a decrease in npp1 expression from 12 to 24 h; at 36 h its expression increased suggesting the existence of a complex mechanism of defense/attack interaction between the pathogen and the host. Expression of recombinant npp1 gene was achieved in Pichia pastoris and assessed by SDS-PAGE analysis of the protein secreted into the culture supernatant, revealing the presence of the NPP1 protein.

Novel approaches and methods for quantifying Phytophthora cinnamomi in avocado tree roots

Phytophthora cinnamomi Rands is a devastating root rot pathogen of avocado. Robust and sensitive root quantification methods are required for determining seasonal P. cinnamomi root colonization patterns and evaluating management strategies. Our study investigated four P. cinnamomi root quantification methods using a newly developed P. cinnamomi-avocado-seedling bioassay system and a P. cinnamomi-specific probe-based qPCR assay. Phytophthora cinnamomi quantification through plating of roots (root plating) or lemon leaf disks obtained from root baitings (root-baiting-plating) onto semi-selective media were the best methods. Root plating consistently yielded significant differences in P. cinnamomi quantities obtained from seedling roots inoculated with five zoospore concentrations (10-1 × 105 zoospores/ml), whereas root-baiting-plating did so less often. The two methods were comparable in yielding root quantities that were significantly correlated with the inoculated zoospore concentrations, rarely yielding false negatives and having the lowest variability between replicates of the same treatment. qPCR quantification from roots was also an effective method; however, treatment replicates were highly variable and false negatives occurred more frequently. The least effective quantification method was qPCR quantification from lemon leaf disks obtained from root baitings.

Silver Nanoparticles and Polyphenol Inclusion Compounds Composites for Phytophthora cinnamomi Mycelial Growth Inhibition

Phytophthora cinnamomi, responsible for "root rot" or "dieback" plant disease, causes a significant amount of economic and environmental impact. In this work, the fungicide action of nanocomposites based on silver nanoparticles and polyphenol inclusion compounds, which feature enhanced bioavailability and water solubility, was assayed for the control of this soil-borne water mold. Inclusion compounds were prepared by an aqueous two-phase system separation method through extraction, either in an hydroalcoholic solution with chitosan oligomers (COS) or in a choline chloride:urea:glycerol deep eutectic solvent (DES). The new inclusion compounds were synthesized from stevioside and various polyphenols (gallic acid, silymarin, ferulic acid and curcumin), in a [6:1] ratio in the COS medium and in a [3:1] ratio in the DES medium, respectively. Their in vitro response against Phytophthora cinnamomi isolate MYC43 (at concentrations of 125, 250 and 500 µg·mL^-1) was tested, which found a significant mycelial growth inhibition, particularly high for the composites prepared using DES. Therefore, these nanocomposites hold promise as an alternative to fosetyl-Al and metalaxyl conventional systemic fungicides.

In Vitro Antifungal Activity of New and Known Geranylated Phenols against Phytophthora cinnamomi Rands

A series of new and known geranylated phenol/methoxyphenol derivatives has been tested in vitro as inhibitor agents of mycelial growth of Phytophthora cinnamomi. The activity of tested compounds is correlated with the nature, number, and position of the substituent group on the aromatic ring. Results indicate that the most active geranylated derivatives are those having two hydroxyl groups (or one –OH and one –OCH₃) attached to the aromatic ring. Interestingly, these derivatives are as active as Metalaxil^®, a commonly used commercial fungicide. Thus, our results suggest that some of these compounds might be of agricultural interest due to their potential use as fungicides against P. cinnamomi. The effect of structure on fungicide activity is discussed in terms of electronic distribution on both the aromatic ring and side geranyl chain. All tested compounds have been synthesized by direct coupling of geraniol and the respective phenol. Interestingly, new digeranylated derivatives were obtained by increasing the reaction time.

Phytophthora cinnamomi

Phytophthora cinnamomi is one of the most devastating plant pathogens in the world. It infects close to 5000 species of plants, including many of importance in agriculture, forestry and horticulture. The inadvertent introduction of P. cinnamomi into natural ecosystems, including a number of recognized Global Biodiversity Hotspots, has had disastrous consequences for the environment and the biodiversity of flora and fauna. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus-like organisms that initiate plant disease through the production of motile zoospores. Disease control is difficult in agricultural and forestry situations and even more challenging in natural ecosystems as a result of the scale of the problem and the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires a comprehensive understanding of the cellular and molecular basis of pathogen development and pathogenicity. The application of next-generation sequencing technologies to generate genomic and transcriptomic data promises to underpin a new era in P. cinnamomi research and discovery. The aim of this review is to integrate bioinformatic analyses of P. cinnamomi sequence data with current knowledge of the cellular and molecular basis of P. cinnamomi growth, development and plant infection. The goal is to provide a framework for future research by highlighting potential pathogenicity genes, shedding light on their possible functions and identifying suitable targets for future control measures.

TAXONOMY

Phytophthora cinnamomi Rands; Kingdom Chromista; Phylum Oomycota or Pseudofungi; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; genus Phytophthora.

HOST RANGE

Infects about 5000 species of plants, including 4000 Australian native species. Host plants important for agriculture and forestry include avocado, chestnut, macadamia, oak, peach and pineapple.

DISEASE SYMPTOMS

A root pathogen which causes rotting of fine and fibrous roots, but which can also cause stem cankers. Root damage may inhibit water movement from roots to shoots, leading to dieback of young shoots. USEFUL WEBSITES: http://fungidb.org/fungidb/; http://genome.jgi.doe.gov/Phyci1/Phyci1.home.html; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314365.1; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314505.1.

Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains. Independent genome assembly produced final genomes of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 82.5% and 81.8% of the eukaryote universal single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analysis and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

BACKGROUND

Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants. Although these important capacities of P. purpurea have been demonstrated, there is no transcriptomic or genomic information available in public databases that could bring insights on the genes underlying this anti-oomycete activity.

RESULTS

Using Illumina technology we obtained a de novo assembly of P. purpurea transcriptome and differential transcript abundance to identify putative defence related genes in challenged versus non-challenged plants. A total of 1,272,600,000 reads from 18 cDNA libraries were merged and assembled into 215,739 transcript contigs. BLASTX alignment to Nr NCBI database identified 124,386 unique annotated transcripts (57.7%) with significant hits. Functional annotation identified 83,550 out of 124,386 unique transcripts, which were mapped to 141 pathways. 39% of unigenes were assigned GO terms. Their functions cover biological processes, cellular component and molecular functions. Genes associated with response to stimuli, cellular and primary metabolic processes, catalytic and transporter functions were among those identified. Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times. Comparative cyto-histological studies of P. purpurea roots challenged with P. cinnamomi zoospores and controls revealed specific morphological features (exodermal strips and epi-cuticular layer), that may provide a constitutive efficient barrier against pathogen penetration. Genes involved in cutin biosynthesis and in exodermal Casparian strips formation were up-regulated.

CONCLUSIONS

The de novo assembly of transcriptome using short reads for a non-model plant, P. purpurea, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies. The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from P. purpurea when challenged with the pathogen. This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with P. cinnamomi.

Pathways to false-positive diagnoses using molecular genetic detection methods; Phytophthora cinnamomi a case study

Phytophthora cinnamomi is one of the world's most invasive plant pathogens affecting ornamental plants, horticultural crops and natural ecosystems. Accurate diagnosis is very important to determine the presence or absence of this pathogen in diseased and asymptomatic plants. In previous studies, P. cinnamomi species-specific primers were designed and tested using various polymerase chain reaction (PCR) techniques including conventional PCR, nested PCR and quantitative real-time PCR. In all cases, the primers were stated to be highly specific and sensitive to P. cinnamomi. However, few of these studies tested their primers against closely related Phytophthora species (Phytophthora clade 7). In this study, we tested these purported P. cinnamomi-specific primer sets against 11 other species from clade 7 and determined their specificity; of the eight tested primer sets only three were specific to P. cinnamomi. This study demonstrated the importance of testing primers against closely related species within the same clade, and not just other species within the same genus. The findings of this study are relevant to all species-specific microbial diagnosis.

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases

The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.

Expression Profiling of Castanea Genes during Resistant and Susceptible Interactions with the Oomycete Pathogen Phytophthora cinnamomi Reveal Possible Mechanisms of Immunity

The most dangerous pathogen affecting the production of chestnuts is Phytophthora cinnamomi a hemibiotrophic that causes root rot, also known as ink disease. Little information has been acquired in chestnut on the molecular defense strategies against this pathogen. The expression of eight candidate genes potentially involved in the defense to P. cinnamomi was quantified by digital PCR in Castanea genotypes showing different susceptibility to the pathogen. Seven of the eight candidate genes displayed differentially expressed levels depending on genotype and time-point after inoculation. Cast_Gnk2-like revealed to be the most expressed gene across all experiments and the one that best discriminates between susceptible and resistant genotypes. Our data suggest that the pre-formed defenses are crucial for the resistance of C. crenata to P. cinnamomi. A lower and delayed expression of the eight studied genes was found in the susceptible Castanea sativa, which may be related with the establishment and spread of the disease in this species. A working model integrating the obtained results is presented.