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Crown gall disease (Agrobacterium tumefaciens), crown/root rot disease (Phytophthora spp.), root lesion disease (Pratylenchus vulnus) and tree vigor are key traits affecting the productivity and quality of walnuts in California. Unchallenged hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that the increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to A. tumefaciens, susceptibility to Phytophthora spp. and increased vigor. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to A. tumefaciens, resistance to Phytophthora spp. and low vigor. Four genes within the J. microcarpa QTL region for resistance to A. tumefaciens and Phytophthora spp. were represented among our transcripts, with two of the genes being differentially expressed in association with resistance to A. tumefaciens and decreased vigor. No differential expression related to Phytophthora spp. or P. vulnus resistance was observed in this region. Additionally, the J. microcarpa haplotype expressed more transcripts associated with resistance to A. tumefaciens, Phytophthora spp. and low vigor, but not P. vulnus, than the J. regia haplotype. We also report unique and shared hormone and defense responses associated with each trait. This research suggests a link between cell wall biogenesis, vigor and critical root diseases of walnut.

Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141 Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility.

Introduction: Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis. Methods: To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analyzed the transcriptome of P. medicaginis across three phases of colonization of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem. Results: The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterization of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death. Discussion: These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase. [ABSTRACT FROM AUTHOR]

Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genomemodel. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility. [ABSTRACT FROM AUTHOR]

AbstractWestern white pine (Pinus monticola) with genetic tolerance to white pine blister rust disease caused by Cronartium ribicola constitutes an invaluable resource for the mitigation of this disease as well as the restoration of the species and its utilization in managed forests. In the last several years, typical root-rot symptoms and sudden tree death have been observed in some western white pine plantations located in British Columbia (BC) in Canada, and a few Phytophthora species were found to be associated with symptomatic trees. Our objectives were to survey one of the plantations located in south-west BC on Vancouver Island to confirm the presence of these Phytophthora species and other oomycetes and test their pathogenicity on western white pine by completing Koch’s postulates. We used direct plating of root samples on PARP(H)-CMA media and by baiting for oomycetes in soil and root samples. Ten oomycetes, including four Phytophthora species (Phytophthora cinnamomi, P. cactorum-like, P. cryptogea and P. pseudocryptogea) were isolated from roots and soil samples of diseased Pi. monticola trees. The Phytophthora species were identified using ITS, β-tubulin and TEF1 gene regions. Koch’s postulates were validated with controlled inoculations of 1-year old seedlings; mortality occurred as early as 15 days after inoculation with P. cinnamomi when the seedlings were maintained in warm temperature conditions (25°C). Molecular typing of two P. cinnamomi cultures using Oxford Nanopore MinIONTM sequencing indicated that they belong to one of the two main clonal clusters of mating type A2 that have been recognized as the main drivers of the global P. cinnamomi epidemic. [ABSTRACT FROM AUTHOR]

Plant pathogens in the genus Phytophthora are a severe threat to forest plantations, ecosystems and tree nurseries. Especially in forests and natural ecosystems, there is a lack of effective measures to control and manage these pathogens. In this study, we conducted a systematic mapping review to collate evidence regarding the control and management of forest Phytophthora in different production settings and ecosystems. The study aimed to reveal possible knowledge gaps, thus guiding future research priorities. We extracted information from nine databases, limiting the search to studies published during the time period from January 2010 to December 2022. The articles were shared between three reviewers who classified the reports using a set of inclusion/exclusion criteria. A total of 561 articles were included and mapped in a database using pre‐defined coding, and critically appraised for relevance and reliability. The analysis showed that biological or bio‐based measures were the most studied interventions, followed by genetics or breeding programmes, whereas chemical and silvicultural management approaches were less studied. Most of the studies were conducted in Europe, North America, Australia and New Zealand. Phytophthora cinnamomi has been the most studied species followed by P. ramorum. We discuss the current knowledge gaps in the implementation of existing research, likely due to a lack of holistic understanding of the processes over time and space, and suggest future research that is needed to manage Phytophthora in forest ecosystems. [ABSTRACT FROM AUTHOR]

SUMMARY: Cucumber plants are highly susceptible to the hemibiotroph oomycete Phytophthora melonis. However, the mechanism of resistance to cucumber blight remains poorly understood. Here, we demonstrated that cucumber plants with impairment in the biosynthesis of brassinosteroids (BRs) or gibberellins (GAs) were more susceptible to P. melonis. By contrast, increasing levels of endogenous BRs or exogenously application of 24‐epibrassinolide enhanced the resistance of cucumber plants against P. melonis. Furthermore, we found that both knockout and overexpression of the BR biosynthesis gene CYP85A1 reduced the endogenous GA3 content compared with that of wild‐type plants under the condition of inoculation with P. melonis, and the enhancement of disease resistance conferred by BR was inhibited in plants with silencing of the GA biosynthetic gene GA20ox1 or KAO. Together, these findings suggest that GA homeostasis is an essential factor mediating BRs‐induced disease resistance. Moreover, BZR6, a key regulator of BR signaling, was found to physically interact with GA20ox1, thereby suppressing its transcription. Silencing of BZR6 promoted endogenous GA biosynthesis and compromised GA‐mediated resistance. These findings reveal multifaceted crosstalk between BR and GA in response to pathogen infection, which can provide a new approach for genetically controlling P. melonis damage in cucumber production. Significance Statement: This study demonstrates that GA homeostasis is necessary for the BRs‐mediated resistance of cucumber to Phytophthora melonis. BZR6, a key regulator of BR signaling, directly suppresses the transcription of GA20ox1 and consequently reduces GA1 and GA3 contents. In conclusion, our results reveal the multifaceted regulation mechanism of BR/GA cooperation in growth–defense trade‐offs. [ABSTRACT FROM AUTHOR]

Background: Pepper Phytophthora blight is a devastating disease during the growth process of peppers, significantly affecting their yield and quality. Accurate, rapid, and non-destructive early detection of pepper Phytophthora blight is of great importance for pepper production management. This study investigated the possibility of using multispectral imaging combined with machine learning to detect Phytophthora blight in peppers. Peppers were divided into two groups: one group was inoculated with Phytophthora blight, and the other was left untreated as a control. Multispectral images were collected at 0-h samples before inoculation and at 48, 60, 72, and 84 h after inoculation. The supporting software of the multispectral imaging system was used to extract spectral features from 19 wavelengths, and textural features were extracted using a gray-level co-occurrence matrix (GLCM) and a local binary pattern (LBP). The principal component analysis (PCA), successive projection algorithm (SPA), and genetic algorithm (GA) were used for feature selection from the extracted spectral and textural features. Two classification models were established based on effective single spectral features and significant spectral textural fusion features: a partial least squares discriminant analysis (PLS_DA) and one-dimensional convolutional neural network (1D-CNN). A two-dimensional convolutional neural network (2D-CNN) was constructed based on five principal component (PC) coefficients extracted from the spectral data using PCA, weighted, and summed with 19-channel multispectral images to create new PC images. Results: The results indicated that the models using PCA for feature selection exhibit relatively stable classification performance. The accuracy of PLS-DA and 1D-CNN based on single spectral features is 82.6% and 83.3%, respectively, at the 48h mark. In contrast, the accuracy of PLS-DA and 1D-CNN based on spectral texture fusion reached 85.9% and 91.3%, respectively, at the same 48h mark. The accuracy of the 2D-CNN based on 5 PC images is 82%. Conclusions: The research indicates that Phytophthora blight infection can be detected 48 h after inoculation (36 h before visible symptoms). This study provides an effective method for the early detection of Phytophthora blight in peppers. [ABSTRACT FROM AUTHOR]

Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant‐damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome‐ and proteome‐level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro‐oxidative stress is also briefly discussed. [ABSTRACT FROM AUTHOR]

Essential oils (EOs) extracted from aromatic and medicinal plants have the potential to inhibit the growth of various pathogens and, thus, be useful in the control of dangerous diseases. The application of environmentally friendly approaches to protect agricultural and forestry ecosystems from invasive and hazardous species has become more significant in last decades. Therefore, the identification and characterization of essential oils with a strong inhibitory activity against aggressive and widespread pathogens are of key importance in plant protection research. The main purpose of our study is to evaluate the impact of essential oils originating from different genotypes of bee balm, mint, and marigold on Botrytis cinerea, Fusarium solani, and Phytophthora pseudocryptogea. Twelve essential oils, including five EOs originating from Monarda fistulosa, one oil each from Monarda russeliana, Mentha longifolia, Mentha piperita, Tagetes patula, and Tagetes erecta, and two EOs from Tagetes tenuifolia were derived by steam or water distillation. The chemical composition of the tested EOs was determined by GS-MS analyses and their corresponding chemotypes were identified. The most effective against all three pathogens were determined to be the EOs originating from M. fistulosa and M. russeliana. B. cinerea, and P. pseudocryptogea were also significantly affected by the M. piperita essential oil. The most efficient EOs involved in this investigation and their potential to control plant pathogens are discussed. [ABSTRACT FROM AUTHOR]

Phytophthora, one among the most devastating phytopathogenic genus representing the oomycetes inflicts substantial damage to a broad spectrum of economically important horticultural crops worldwide. The rapid dissemination of Phytophthora in agro-ecosystems is mediated through bi-flagellated zoospores and their homing response towards the host is profoundly influenced by chemo-electrotactic mechanisms leading to encystment and subsequent colonization. Though different procedures are reported to isolate Phytophthora from infested rhizospheric soils, studies addressing zoospore encystment-based method using different baits for isolation and subsequent retrieval of cultures (in case of bacterial contamination) are meagre in Phytophthora-black pepper host-pathosystem. In the present study, Phytophthora was isolated from infested rhizospheric soils of black pepper using different baits viz., thermocol, impregnated paper discs, leaves of Albizzia falcataria and green gram roots. Modified cabin-sequestering methods were subsequently adopted to salvage the cultures in case of bacterial contamination, if any. The zoospore encystment-based method is cost effective and consumes lesser time for isolation of Phytophthora from infested rhizospheric soils of black pepper. Further, the two approaches of cabin sequestering method which were found promising in obtaining pure cultures of Phytophthora devoid of bacterial contamination, can also be employed to retrieve bacterial contaminated cultures of research significance. [ABSTRACT FROM AUTHOR]

To prevent threats from pathogens such as Phytophthora species from international plant trade, molecular identification techniques are needed for rapid, accurate quarantine inspection. Here, for quarantine control in Japan, we developed a simple DNA extraction for plants and a practical detection method that combines multiplexed PCR using primers specific for Phytophthora species, for P. nicotianae, which is the only non-quarantine Phytophthora species, and as internal controls, for plants. For the new genus-level primer set, we modified previously reported genus-specific primers to improve detectability. The new primers were able to detect mycelial DNA of 155 taxa among Phytophthora clades 1–10, with a sensitivity of 100 fg/µL for three representative species, P. ramorum, P. kernoviae and P. nicotianae. In the PCRs using DNA from non-target species, amplification was observed for only three taxa, and for some strains, four taxa in a closely related genus. Duplex and triplex PCR of the genus-specific primers combined with previously reported plant primers verified the success of DNA extraction and PCR detection from diseased plant samples, and in the triplex PCR, whether the pathogen was diagnosed as P. nicotianae or not by the species-specific primer. The new method detected the pathogen in naturally infected and inoculated plants. The amplicons using the genus-specific primer have enough variation to be sequenced to identify the species. This new method can be used immediately for detecting Phytophthora species and for quarantine control in Japan. [ABSTRACT FROM AUTHOR]

Late blight, caused by the notorious pathogen Phytophthora infestons, poses a significant threat to potato (Solanum tuberosum) crops worldwide, impacting their quality as well as yield. Here, we aimed to investigate the potential use of cinnamaldéhyde, carvacrol, and eugenol as control agents against P. infestons and to elucidate their underlying mechanisms of action. To determine the pathogen-inhibiting concentrations of these three plant essential oils (PEOs), a comprehensive evaluation of their effects using gradient dilution, mycelial growth rate, and spore germination methods was carried out. Cinnamaldéhyde, carvacrol, and eugenol were capable of significantly inhibiting P. infestons by hindering its mycelial radial growth, zoospore release, and sporangium germination; the median effective inhibitory concentration of the three PEOs was 23.87. 8.66, and 89.65 pl/liter, respectively. Scanning electron microscopy revealed that PEOs caused the irreversible deformation of P. infestons, resulting in hyphal shrinkage, distortion, and breakage. Moreover, propidium iodide staining and extracellular conductivity measurements demonstrated that all three PEOs significantly impaired the integrity and permeability of the pathogen's ceil membrane in a time- and dose-dependent manner. In vivo experiments confirmed the dose-dependent efficacy of PEOs in reducing the lesion diameter of potato late blight. Altogether, these findings provide valuable insight into the antifungal mechanisms of PEOs vis-à-vis late blight-causing P. infestons. By utilizing the inherent capabilities of these natural compounds, we could effectively limit the harmful impacts of late blight on potato crops, thereby enhancing agricultural practices and ensuring the resilience of global potato food production. [ABSTRACT FROM AUTHOR]

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The biocontrol potential of three native soil cyanobacteria from biological soil crusts (Nostoc commune, Scytonema hyalinum, and Tolypothrix distorta) was tested by means of in vitro mycelial growth inhibition assays for eighteen cyanobacteria-based products against three phytopathogenic soilborne fungi (Phytophthora capsici, Pythium aphanidermatum, and Fusarium oxysporum f. sp. radicis-cucumerinum). Three cyanobacteria-based production factors were considered: (i) cyanobacterium strain, (ii) cyanobacterial culture growth phase, and (iii) different post-harvest treatments: raw cultures, cyanobacterial filtrates, and cyanobacterial extracts. Results showed that any of the factors considered are key points for successfully inhibiting fungal growth. N. commune showed the highest growth inhibition rates for the three phytopathogens; stationary phase treatments produced higher inhibition percentages than logarithmic ones; and all the post-harvest treatments of N. commune at the stationary phase inhibited the growth of P. capsici, up to 77.7%. Thus, N. commune products were tested in planta against P. capsici, but none of the products showed efficacy in delaying the onset nor reducing the damage due to P. capsici, demonstrating the complexity of the in planta assay's success and encouraging further research to design an appropriate scaling up methodology. [ABSTRACT FROM AUTHOR]

ABSTRACTStrawberry growers across the United States are looking for sustainable alternatives to conventional pesticides for management of soil-borne or crown-rot causing pathogens, such as plant-extracts like thyme oil. The objectives of this study were to determine the impact of soil-applied thyme oil fungicides on strawberry plant health, yield, sweetness, and foliar disease, and on the assemblage of soil microbial communities in strawberry plasticulture systems. In 2021 and 2022 the interaction of three soil-applied fungicides and three foliar fungicide programs were explored. Thyme oil was not found to improve strawberry plant growth or yield when compared to strawberries in the control. However, plants treated with mefenoxam exhibited an average winter crown weight of 2.11 g, significantly lower than control and thyme oil treatments at 3.14 g and 3.16 g, respectively. This translated into a significant yield loss where mefenoxam treated plants exhibited lowered yields at 416.04 g of fruit per plant compared to 523.57 g and 521.53 g per plant in the control and thyme oil treatments, respectively. A high incidence of foliar and fruit diseases was present; however, no interaction of soil and foliar fungicide treatments were observed for yield or fruit sweetness. Minimal root protection from pathogens was observed for all treatments and Fusarium, Pythium and Phytophthora fungi were regularly observed. Mefenoxam was observed to increase the recovery of oomycetes, which may cause Pythium and Phytophthora. No benefit from thyme oil was observed at our site and its addition as a soil fungicide would likely not benefit most growers.

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

Research on reducing the movement of pests on wood products has led to several options for safer trade including heat treatment of wood to mitigate pests. In this study, pathogenic organisms commonly regulated in the trade of forest products were tested to determine the minimum heat dose (temperature and time) required to cause mortality. The mycelial stage of tree pathogens, Heterobasidion occidentale, Grosmannia clavigera, Bretziella fagacearum, Phytophthora cinnamomi, P. lateralis, P. ramorum and P. xmultiformis, which may be found in untreated wood products, were tested in vitro using the Humble water bath with parameters simulating the rate of heat applied to wood in a commercial kiln. RNA detection using reverse transcription real-time PCR was used to validate pathogen mortality following treatment for: P. ramorum, P. lateralis, P. cinnamomi, P. xmultiformis and G. clavigera. The lethal temperature for all pathogens ranged from 44 to 50°C for a 30-min treatment duration. Using this method to evaluate heat treatment for other forest product pests is recommended to accurately identify the minimum dose required to support phytosanitary trade. With more data potentially lower heat treatment applications may be recommended under specific conditions to produce more efficient and economical heat treatment schedules and reduce environmental impacts. [ABSTRACT FROM AUTHOR]

Phytophthora sojae is a devastating plant pathogen that causes soybean Phytophthora root rot worldwide. Early on-site and accurate detection of the causal pathogen is critical for successful management. In this study, we have developed a novel and specific one-pot RPA/PCR-CRISPR/Cas12 assay for onsite detection (Cas-OPRAD) of Phytophthora root rot (P. sojae). Compared to the traditional RPA/PCR detection methods, the Cas-OPRAD assay has significant detection performance. The Cas-OPRAD platform has excellent specificity to distinguish 33 P. sojae from closely related oomycetes or fungal species. The PCR-Cas12a assay had a consistent detection limit of 100 pg. µL-1, while the RPA-Cas12a assay achieved a detection limit of 10 pg. µL-1. Furthermore, the Cas-OPRAD assay was equipped with a lateral flow assay for on-site diagnosis and enabled the visual detection of P. sojae on the infected field soybean samples. This assay provides a simple, efficient, rapid (<1 h), and visual detection platform for diagnosing Phytophthora root rot based on the one-pot CRISPR/Cas12a assay. Our work provides important methods for early and accurate onsite detection of Phytophthora root rot in the field or customs fields. [ABSTRACT FROM AUTHOR]

Soybean production is significantly impacted by Phytophthora root rot (PRR), which is caused by Phytophthora sojae. The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean NLR genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the NLR gene (Glyma.18g283200) were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after P. sojae infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and Glyma.18g283200 overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to P. sojae infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to P. sojae at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR. [ABSTRACT FROM AUTHOR]

Phytophthora cactorum is a plant pathogenic oomycete that causes crown rot in strawberry leading to significant economic losses every year. To invade the host, P. cactorum secretes an arsenal of effectors that can manipulate host physiology and impair its defense system promoting infection. A transcriptome analysis was conducted on a susceptible wild strawberry genotype (Fragaria vesca) 48 hours post inoculation with P. cactorum to identify effectors expressed during the early infection stage. The analysis revealed 4,668 P. cactorum genes expressed during infection of F. vesca. A total of 539 secreted proteins encoded by transcripts were identified, including 120 carbohydrate-active enzymes, 40 RXLRs, 23 proteolytic enzymes, nine elicitins, seven cysteine rich proteins, seven necrosis inducing proteins and 216 hypothetical proteins with unknown function. Twenty of the 40 RXLR effector candidates were transiently expressed in Nicotiana benthamiana using agroinfiltration and five previously unreported RXLR effector genes (Pc741, Pc8318, Pc10890, Pc20813, and Pc22290) triggered cell death when transiently expressed. The identified cell death inducing RXLR effectors showed 31-66% identity to known RXLR effectors in different Phytophthora species having roles in pathogenicity including both activation and suppression of defense response in the host. Furthermore, homology analysis revealed that these cell death inducing RXLR effectors were highly conserved (82 - 100% identity) across 23 different strains of P. cactorum originating from apple or strawberry. [ABSTRACT FROM AUTHOR]

Cucumber blight is a destructive disease. The best way to control this disease is resistance breeding. This study focuses on disease resistance gene mapping and molecular marker development.We used the resistant cucumber, JSH, and susceptible cucumber, B80, as parents to construct F2 populations. Bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF‐seq) were used, from which we developed cleaved amplified polymorphic sequence (CAPs) markers to map the resistance gene.Resistance in F2 individuals showed a segregation ratio of resistance:susceptibility close to 3:1. The gene in JSH resistant cucumber was mapped to an interval of 9.25 kb, and sequencing results for the three genes in the mapped region revealed three mutations at base sites 225, 302, and 591 in the coding region of Csa5G139130 between JSH and B80, but no mutations in coding regions of Csa5G139140 and Csa5G139150. The mutations caused changes in amino acids 75 and 101 of the protein encoded by Csa5G139130, suggesting that Csa5G139130 is the most likely resistance candidate gene. We developed a molecular marker, CAPs‐4, as a closely linked marker for the cucumber blight resistance gene.This is the first report on mapping of a cucumber blight resistance gene and will provideg a useful marker for molecular breeding of cucumber resistance to Phytophthora blight. [ABSTRACT FROM AUTHOR]

Seven Phytophthora isolates were recovered from roots and rhizosphere soil of different plants of the Bajaur, a newly merged district in Khyber Pakhtunkhwa province of Pakistan. These isolates were characterized morphologically as well as molecularly using internal transcribed spacer (ITS) sequences and of them identified are Phytophthora lacustris, Phytophthora capsici, Phytophthora citrophthora and Phytophthora nicotianae. P. lacustris appeared to be a new record from Pakistan not hitherto reported. P. nicotianae and P. citrophthora are reported for the first time from the rhizosphere of Isodon rugosus and Cajanus cajan in Pakistan. [ABSTRACT FROM AUTHOR]

Natural resource management can struggle with increased visitation that inadvertently deteriorates the environment. In Aotearoa New Zealand, visitors to kauri forests are spreading a lethal soil pathogen resulting in cultural and conservation risk. While public awareness of kauri dieback disease is growing, compliance at hygiene stations has not similarly increased. To overcome this apparent knowledge-behaviour gap, five interventions (ambassadors, normative messaging, watching eye effect, hazard perception, and pledge board) were evaluated for their impact on visitor compliance with footwear/equipment cleaning behaviour. Behavioural observations (n = 10,536) and intercept surveys (n = 3,061) were collected. Ambassadors resulted in increased compliance for both visitors and local trail users. The pledge board resulted in increased compliance for local trail users only and normative message increased compliance at one visitor site. Hazard perception and watching eye resulted in a decrease in compliance behaviour. This research demonstrates the need for careful assessment of interventions designed to mitigate the impacts of visitors to conservation areas. The success of the ambassador intervention, the pledge board for locals and, to a lesser extent, the normative message at one location, offer field-based empirical evidence supporting the use of social norms in communication approaches aimed at influencing visitor behaviour in natural resource settings. [ABSTRACT FROM AUTHOR]

A number of Phytophthora species have been identified as destructive plant pathogens and invasive species. They have the potential to affect a wide range of host plants and cause diseases in agricultural and forest ecosystems. Two Phytophthora species from rhizosphere soil samples collected from declining Alnus glutinosa in Bulgaria were isolated in the autumn of 2022. They were identified as Phytophthora polonica and Phytophthora hydropathica according to the DNA sequence analysis of the ITS region, as well as their morphological and physiological characteristics. The pathogenicity of both species to common and gray alder was evaluated by the inoculation of detached leaves and cuttings. Experimental data proved that P. polonica and P. hydropathica are able to cause leaf necrosis not only on A. glutinosa from which they were derived, but also on A. incana. No significant deference in the aggressiveness of the studied isolates from both Phytophthora species against the two tested plants was observed. Therefore, P. polonica and P. hydropathica were determined as potential threats for alder ecosystems in the country. This is the first report for the isolation of P. polonica in Bulgaria and represents the most southeastern point of the species distribution in Europe. [ABSTRACT FROM AUTHOR]

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

Vanda is a highly valued and important orchid in the horticultural industry; however, it is usually damaged by black rot disease, caused by Phytophthora species, leading to substantial economic losses. This study aims to evaluate multiple fungicides for black rot control. Oomycetes were isolated from diseased plants, and these isolates brought about a 100% disease incidence in Vanda with water-soaked lesions, becoming necrotic within 24 h. The isolates were identified as Phytophthora palmivora based on a phylogenetic analysis of internal transcribed spacers (ITSs) and cytochrome oxidase spacer regions. For controlling black rot disease, eight fungicides or mixtures with different target sites and modes of action were screened, including cyazofamid, dimethomorph, fosetyl-aluminum, metalaxyl, thiophanate-methyl, a mixture of fluopicolide and fosetyl-aluminum, a mixture of mancozeb and valifenalate, and a mixture of quintozene and etridiazole. All tested fungicides showed 33%–100% growth inhibition using the poisoned food technique. In greenhouse experiments, seven tested fungicide formulations, except for thiophanate-methyl, exhibited 20%–66% reduced lesion sizes compared with the no-chemical control. The information on fungicides with different filicide group codes could assist a fungicide spray program for black rot management in orchids. [ABSTRACT FROM AUTHOR]

Phytophthora root rot (PRR) of chickpea (Cicer arietinum) caused by Phytophthora medicaginis is an important disease. Partial resistance to PRR is sourced from Cicer echinospermum. In this study, we evaluated if lines with low levels of PRR foliage symptoms in two contrasting recombinant inbred line (RIL) populations parented by chickpea cultivars (Yorker and Rupali) and 04067-81-2-1-1 (C. echinospermum, interspecific breeding line) had a significant drag on yield parameters. For the Yorker × 04067-81-2-1-1 population with the highest level of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly later flowering and podding, lower grain yields, and lighter seed and shorter plant phenotypes than high foliage symptom RIL. A quantitative trait locus analysis identified significant QTL for flowering, height, 100-seed weight, and yield, and there was a significantly higher frequency of alleles for the negative agronomic traits (i.e., drag) from the 04067-81-2-1-1 parent in low foliage symptom RIL than in high foliage symptom RIL. For the Rupali × 04067-81-2-1-1 population with lower levels of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly lighter seed and shorter plants than high foliage symptom RIL. Significant QTL were detected, the majority were for the timing of flowering and podding (n = 18), others were for plant height, yield, and 100-seed weight. For this second population, the frequency of alleles for the negative agronomic traits from the 04067-81-2-1-1 parent did not differ between low and high foliage symptom RIL. The 100 seed weight of RIL under moderate PRR disease pressure showed some promise as a yield component trait to identify phenotypes with both high levels of PRR resistance and grain yield potential for further seed number evaluations. We identified that large population sizes are required to enable selection among chickpea × C. echinospermum crosses for high levels of PRR resistance without a significant drag on yield. [ABSTRACT FROM AUTHOR]

Phytophthora nicotianae is a global and polyphagous pathogen with a wide host range. P. nicotianae can infect Areca catechu, Durio zibethinus L., Psidium guajava L., Hevea brasiliensis, and other tree species. The pathogen is capable of inducing butt rot and affecting aerial parts, including stems, leaves, and fruits. Compared to other Phytophthora species, P. nicotianae is more adaptable to abiotic stress. In this study, recombinase polymerase amplification (RPA) in combination with the CRISPR/Cas12a system was used for the detection of P. nicotianae, and achieved rapid and efficient detection of P. nicotianae. The assay was highly specific to P. nicotianae. All 4 tested isolates of P. nicotianae yielded positive results, whereas 30 isolates belonging to 17 other Phytophthora species, 8 fungal species, and 4 Bursaphelenchus xylophilus vermicules lacked detection. Under the conditions of 37 °C, after 20 min of RPA reaction and 25 min of Cas12a cleavage, a DNA concentration as low as 10 pg·μL−1 could be detected. In addition, it detected P. nicotianae from artificially inoculated leaves of Fatsia japonica. In this study, a novel method was established for the efficient and accurate detection of P. nicotianae based on the combination of RPA and the CRISPR/Cas12a system. [ABSTRACT FROM AUTHOR]

Avocado tree wilt is a disease caused by Phytophthora cinnamomi Rands. Recently, this disease has been associated to Pythium amazonianum, another causal agent. Avocado tree wilt is being currently controlled with synthetic fungicides that kill beneficial microorganisms, polluting the environment and leading to resistance problems in plant pathogens. The current research work aims to provide alternative management using extracts from Proboscidea parviflora W. and Phaseolus lunatus L. to control the development of mycelia in P. amazonianum in vitro. Raw extracts were prepared at UAAAN Toxicology Laboratory, determining the inhibition percentages, inhibition concentrations and inhibition lethal times. Several concentrations of the plant extracts were evaluated using the poisoned medium methodology, showing that both extracts control and inhibit mycelial development, in particular P. lutatus, which inhibits mycelial growth at concentrations lower than 80 mg/L, being lower than P. parviflora extracts. These extracts are promising candidates for excellent control of Pythium amazonianum. [ABSTRACT FROM AUTHOR]

Summary: Nonmycorrhizal cluster root‐forming species enhance the phosphorus (P) acquisition of mycorrhizal neighbours in P‐impoverished megadiverse systems. However, whether mycorrhizal plants facilitate the defence of nonmycorrhizal plants against soil‐borne pathogens, in return and via their symbiosis, remains unknown.We characterised growth and defence‐related compounds in Banksia menziesii (nonmycorrhizal) and Eucalyptus todtiana (ectomycorrhizal, ECM) seedlings grown either in monoculture or mixture in a multifactorial glasshouse experiment involving ECM fungi and native oomycete pathogens.Roots of B. menziesii had higher levels of phytohormones (salicylic and jasmonic acids, jasmonoyl‐isoleucine and 12‐oxo‐phytodienoic acid) than E. todtiana which further activated a salicylic acid‐mediated defence response in roots of B. menziesii, but only in the presence of ECM fungi. We also found that B. menziesii induced a shift in the defence strategy of E. todtiana, from defence‐related secondary metabolites (phenolic and flavonoid) towards induced phytohormone response pathways.We conclude that ECM fungi play a vital role in the interactions between mycorrhizal and nonmycorrhizal plants in a severely P‐impoverished environment, by introducing a competitive component within the facilitation interaction between the two plant species with contrasting nutrient‐acquisition strategies. This study sheds light on the interplay between beneficial and detrimental soil microbes that shape plant–plant interaction in severely nutrient‐impoverished ecosystems. [ABSTRACT FROM AUTHOR]

Background: Phytophthora sojae, a soil-borne oomycete pathogen, has been a yield limiting factor for more than 60 years on soybean. The resurgence of P. sojae (Phytophthora sojae) is primarily ascribed to the durable oospores found in soil and remnants of the disease. P. sojae is capable of infesting at any growth periods of the soybean, and the succeed infestation of P. sojae is predominantly attributed to long-lived oospores present in soil. Comprehending the molecular mechanisms that drive oospores formation and their significance in infestation is the key for effective management of the disease. However, the existing challenges in isolating and extracting significant quantities of oospores pose limitations in investigating the sexual reproductive stages of P. sojae. Results: The study focused on optimizing and refining the culture conditions and extraction process of P. sojae, resulting in establishment of an efficient and the dependable method for extraction. Novel optimized approach was yielded greater quantities of high-purity P. sojae oospores than traditional methods. The novel approach exceeds the traditional approaches with respect to viability, survival ability, germination rates of new oospores and the pathogenicity of oospores in potting experiments. Conclusion: The proposed method for extracting P. sojae oospores efficiently yielded a substantial quantity of highly pure, viable, and pathogenic oospores. The enhancements in oospores extraction techniques will promote the research on the sexual reproductive mechanisms of P. sojae and lead to the creation of innovative and effective approaches for managing oomycete diseases. [ABSTRACT FROM AUTHOR]

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

Castor bean (Ricinus communis) is a crop of great economic importance in Brazil. It is used for producing oil used in the manufacture of cosmetics and biodiesel. The genus Phytophthora contains pathogens with a wide range of host plants, including ornamentals, fruit and vegetable crops. Among the symptoms induced by Phytophthora species are collar and root rot. This study aimed to identify Phytophthora species causing collar and root rot in castor bean seedlings in the Federal District and test their pathogenicity. Samples of symptomatic plants were collected in four satellite cities in Distrito Federal, Brazil. Fourteen isolates were obtained, and they were initially identified through the morphology of reproductive structures. The isolates were subjected to molecular characterization using phylogeny of the sequences from the ITS region and the Cytochrome Oxidase II gene. Ten isolates of the pathogen were tested for pathogenicity on seedlings of two castor bean accessions and species known to be hosts of P. nicotianae. The isolates were identified as P. nicotianae (12 isolates) and P. palmivora (two isolates). In the pathogenicity test, all isolates were capable of causing disease in castor beans. The isolates of P. nicotianae and P. palmivora varied in pathogenicity to other plant species. This is the first report of P. nicotianae causing collar and root rot in castor bean in the Central‐West Region of Brazil. It is also the first report of P. palmivora causing diseases in castor beans in South America. [ABSTRACT FROM AUTHOR]

Mortality of Nothofagus trees in native forests in Chile has been observed for more than 30 years. Phytophthora pseudosyringae was identified as the causal agent of partial defoliation and bleeding cankers on Nothofagus obliqua and N. alpina. Nevertheless, to improve the conservation of natural resources it is crucial to determine potential native hosts that may act as inoculum reservoirs. Two N. obliqua stands were visited and all native plant species with symptoms resembling those caused by Phytophthora spp. were examined. Seven isolates from cortical and foliar tissues were isolated and subsequentially identified as P. pseudosyringae. Pathogenicity tests were carried out on eight species from a native forest. P. pseudosyringae caused cankers in N. obliqua, N. dombeyi and Persea lingue. Under natural conditions, no symptoms were detected on leaves of Cryptocarya alba, N. dombeyi, N. obliqua or Peumus boldus, but lesions were formed in inoculation assays under a controlled environment, suggesting that these species may act as hosts. Leaf necrosis in P. lingue was observed in both natural and controlled conditions. P. pseudosyringae can sporulate on lesions of C. alba, N. dombeyi and N. obliqua leaves. In Sophora macrocarpa, sporulation was observed both on asymptomatic tissues and on lesions. The frequent association of S. macrocarpa in the understorey of Nothofagus spp. strengthens the putative role of S. macrocarpa as an inoculum reservoir for epidemic events in Nothofagus. This is the first study carried out in the Southern Hemisphere on the life cycle of P. pseudosyringae in native Nothofagus forests. [ABSTRACT FROM AUTHOR]

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

This review deals with major diseases caused by fungi and oomycetes in the citrus supply chain, including post-harvest fruit diseases, and summarizes the strategies and techniques that may be adopted to prevent the damages and losses they cause. Its scope is to highlight the contribute that smart technologies provide towards new solutions for sustainable and safe management strategies of these diseases. Particular attention is given to the application of biopesticides, natural substances, resistance inducers and biostimulants to prevent fruit rots. The review focuses also on mycotoxins and mycotoxigenic fungi that contaminate fresh fruit and food products derived from citrus fruit, an aspect that has been little investigated and regulated so far. An additional relevant aspect addressed by the review is the early detection and routine diagnosis of fungal and oomycete pathogens that threat the international trade and long-distance shipment of citrus fruit, with a particular emphasis on quarantine pathogens. In this respect, the opportunities offered by new practical, rapid, sensitive and robust molecular diagnostic methods are briefly discussed. [ABSTRACT FROM AUTHOR]

Understanding the knowledge and behavior of nonindustrial private forest landowners towards Port-Orford cedar (POC) root disease (Phytophthora lateralis), sudden oak death (Phytophthora ramorum), and disease-resistant seedlings can help target effective education and outreach programs. We surveyed two counties in Southern Oregon to gain knowledge about these pathogens, disease-resistant seedlings, landowner behavior, and landowner preferences regarding planting disease-resistant seedlings. Amenity-based management objectives were more associated with planting disease-resistant POC. Respondents were more likely to plant disease-resistant conifers than hardwoods. Disease-resistant planting preferences were associated with years owned and acres of ownership. Designing targeted education and outreach programs will be necessary to achieve broad scale adoption of disease management and restoration practices. Study implications: We present results from a survey of nonindustrial private forest (NIPF) landowners in two counties in Southern Oregon to determine general landowner characteristics and knowledge of two nonnative diseases, Port-Orford cedar root disease, caused by Phytophthora lateralis , and sudden oak death, caused by Phytophthora ramorum. NIPF landowners play meaningful roles in invasive disease management: recognizing and reporting symptoms of nonnative plant diseases with the objective of early detection and control, implementing management actions to help mitigate disease spread, and planting disease-resistant seedlings during restoration efforts. Understanding landowner knowledge about diseases is important for engaging them in insect and disease mitigation. [ABSTRACT FROM AUTHOR]

In this study, greenhouse tests were conducted on 240 Fraxinus excelsior seedlings to investigate the simultaneous damage caused by thea pathogenic fungus and oomycetes. The experiment was performed under controlled conditions in the greenhouse of the Institute of Forest Research in Sękocin Stary (Poland). Three species of oomycetes were used for the experiment: Phytophthora plurivora, Phytophthora taxon hungarica, Phytophthora megasperma, and the fungus Hymenoscyphus fraxineus. Inoculations using the fungus were carried out on shoots and in plant pots in which the soil was mixed with the three Phytophthora species mentioned above, both simultaneously and separately, which made it possible to recognize the cumulative effect of the related plant infection. The aim of the study was to investigate the effect of phosphite-containing preparations on the health of common ash under conditions of threat to the roots by Phytophthora spp. and damage to the aerial parts of the plant by the fungus, as well as the possible occurrence of synergistic effects. Two types of protective preparations (Actifos and Phos60 of the nitrogen and potassium forms, respectively) were used. It was found that the inoculation of ash seedlings with the fungus H. fraxineus resulted in plant mortality, while the mixture of Phytophthora did not cause significant damage. It was confirmed that when pathogens coexist, a phenomenon occurs that leads to an acceleration in the development of disease symptoms and, thus, to plant mortality. In vitro tests confirmed the usefulness of phosphite preparations for the protection of ash seedlings. [ABSTRACT FROM AUTHOR]

Background: Phytophthora cinnamomi is one of the soil-borne pathogens that causes root rot and stem rot in many plants globally. P. cinnamomi has serious economic, social, and environmental impacts, threatening natural ecosystems and biodiversity. Methods: In this study, a molecular detection method based on Recombinant polymorphic amplification (RPA) combined using the CRISPR/Cas12a system was developed for P. cinnamomi. The method was found to be highly specific for P. cinnamomi. Results: The results showed that 10 P. cinnamomi isolates were positive; however, 21 Phytophthora species, 4 Phytopythium species, 18 fungal species, and 2 Bursaphelenchus species were negative. In total, 10 pg·µL−1 of P. cinnamomi genomic DNA can be detected. The detection process is performed within 20 min at 37 °C, which makes it fast and convenient for use. Discussion: In conclusion, the RPA-CRISPR/Cas12a system in this study is a promising tool for the rapid and sensitive detection of P. cinnamomi in plant samples. [ABSTRACT FROM AUTHOR]

Studies of Phytophthora impact in forests generally focus on individual species without recognition that Phytophthora occur in multispecies communities. This study investigated community structure of Phytophthora species in the rhizosphere of Agathis australis (kauri) in Te Wao Nui o Tiriwa/Waitākere Ranges, New Zealand, in the context of kauri dieback disease expression. Soil sampling and tree monitoring were conducted on 767 randomly selected mature kauri trees. Phytophthora species were detected using both soil baiting and DNA metabarcoding of environmental DNA (eDNA). Four species were detected with soil baiting (P. agathidicida, P. cinnamomi, P. multivora, and P. pseudocryptogea/P. cryptogea) and an additional three species with metabarcoding (P. kernoviae, P. cactorum/P. aleatoria and an unknown clade 7 species). Phytophthora cinnamomi was the most abundant species and was distributed throughout the forest. Both P. multivora and P. agathidicida were limited to forest edges, suggesting more recent introductions. P. agathidicida presence was strongly correlated with declining canopy health, confirming its role as the main driver of kauri dieback. The limited distribution of P. agathidicida and infrequent detections (11.0% samples) suggests that that this species is spreading as an introduced invasive pathogen and provide hope that with strategic management (including track upgrades and closures, restricting access to uninfected areas, and continual monitoring) uninfected areas of the forest can be protected. The frequent detections of P. cinnamomi and P. multivora from symptomatic trees in the absence of P. agathidicida suggest more research is needed to understand their roles in kauri forest health. [ABSTRACT FROM AUTHOR]

There are several highly damaging Phytophthora species pathogenic to forest trees, many of which have been spread beyond their native range by the international trade of live plants and infested materials. Such introductions can be reduced through the development of better tools capable of the early, rapid, and high-throughput detection of contaminated plants. This study utilized a volatilomics approach (solid-phase microextraction coupled to gas chromatography–mass spectrometry) to differentiate between several Phytophthora species in culture and discriminate between healthy and Phytophthora-inoculated European beech and pedunculate oak trees. We tentatively identified 14 compounds that could differentiate eight Phytophthora species from each other in vitro. All of the Phytophthora species examined, except Phytophthora cambivora, uniquely produced at least one compound not observed in the other species; however, most detected compounds were shared between multiple species. Phytophthora polonica had the most unique compounds and was the least similar of all the species examined. The inoculated seedlings had qualitatively different volatile profiles and could be distinguished from the healthy controls by the presence of isokaurene, anisole, and a mix of three unknown compounds. This study supports the notion that volatiles are suitable for screening plant material, detecting tree pathogens, and differentiating between healthy and diseased material. [ABSTRACT FROM AUTHOR]

Plant cells undergo extensive transcriptional reprogramming following pathogen infection, with these reprogramming patterns becoming more complex when pathogens, such as hemibiotrophs, exhibit different lifestyles. These transcriptional changes are often orchestrated by MYB, WRKY and AP2/ERF transcription factors (TFs), which modulate both growth and defence‐related gene expression. Transcriptional analysis of defence‐related genes in avocado (Persea americana) infected with Phytophthora cinnamomi indicated differential immune response activation when comparing a partially resistant and susceptible rootstock. This study identified 226 MYB, 82 WRKY, and 174 AP2/ERF TF‐encoding genes in avocado, using a genome‐wide approach. Phylogenetic analysis revealed substantial sequence conservation within TF groups underscoring their functional significance. RNA‐sequencing analysis in a partially resistant and susceptible avocado rootstock infected with P. cinnamomi was indicative of an immune response switch occurring in either rootstock after 24 and 6 h post‐inoculation, respectively. Different clusters of co‐expressed TF genes were observed at these times, suggesting the activation of necrotroph‐related immune responses at varying intervals between the two rootstocks. This study aids our understanding of avocado immune response activation following P. cinnamomi infection, and the role of the TFs therein, elucidating the transcriptional reprogramming disparities between partially resistant and susceptible rootstocks. [ABSTRACT FROM AUTHOR]

Phytophthora pseudosyringae is a self‐fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping‐by‐sequencing. Coalescent‐based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide. [ABSTRACT FROM AUTHOR]

Phytophthora gummosis, foot rot, and root rot are considered major challenges to the citrus industry worldwide. Little is known about the Phytophthora–microbiome interaction, despite several studies demonstrating changes in the microbial composition of the rhizosphere following challenges by a pathogen. In the present study, we studied the microbial diversity and community structure in healthy rhizospheres and Phytophthora-infected rhizospheres of Khasi mandarin (Citrus reticulata Blanco), a commercial cultivar extensively grown in the northeast of India. An exploratory study was conducted to identify Phytophthora-infected orchards of Khasi mandarin, and the isolated pathogen was confirmed as P. nicotianae based on its morpho-cultural and molecular characteristics coupled with pathogenicity tests. This study on culturable microbes established the dominance of Trichoderma spp. in the healthy rhizosphere, while the diseased rhizosphere showed the presence of Fusarium spp. A metagenomic study further revealed that the rhizospheres of Phytophthora-infected plants were dominated by species such as Bacteroidia spp., Patescibacteria spp., and Pythium spp., while the healthy Khasi mandarin rhizospheres had a more diverse community predominantly represented by Trichoderma, Penicillium, Linnemannia, Mortierella, Talaromyces, Saitozyma, Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Terrabacteria and FCB (Fibrobacterota, Chlorobiota, and Bacteroidota groups) were found to exist in higher relative abundance in disease-free soils than in Phytophthora-infected soils, while phylum Proteobacteria showed identical relative abundance in all soil types. The phyla represented by Pseudomonas, Flavobacteriia, Candidatus, Mycobacterium, Rhizobium, Mesorhizobium, Sphingomonas, and Cytophagia were the most common bacterial phyla in all soil samples, but healthy soil exhibited a greater abundance of Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Our study suggests that the presence of Phytophthora spp. in the rhizosphere alters microbial community structure, having potentially strong implications for plant health and productivity. These rhizosphere microbiome-derived citrus responses shed light on exploring effective management strategies for Phytophthora gummosis disease ailing Khasi mandarin. [ABSTRACT FROM AUTHOR]

Aims Determine the wheat rhizosphere competence of Trichoderma gamsii strain A5MH and in planta suppression of the Pythium root and Fusarium crown rot pathogens Globisporangium irregulare and Fusarium pseudograminearum. Methods and results Wheat was continuously cropped (eight years) at a minimum tillage, low growing season rainfall (GSR ≤ 170 mm) site shown as highly conducive to Pythium root and Fusarium crown rots. Root isolation frequency (RIF) and qPCR were used to determine the rhizosphere dynamics of strain A5MH and the target pathogens at tillering, grain harvest, and in postharvest stubble over the final 2 years. Strain A5MH actively colonized the wheat rhizosphere throughout both growing seasons, had high root abundance at harvest [log 4.5 genome copies (GC) g−1] and persisted in standing stubble for at least 293-d postinoculation. Globisporangium irregulare was most abundant in roots at tillering, whereas F. pseudograminearum was only abundant at harvest and up to 9-fold greater in the drier, second year (GSR 105 mm). Strain A5MH decreased RIF of both pathogens by up to 40%, root abundance of G. irregulare by 100-fold, and F. pseudogaminearum by 700-fold, but was ineffective against crown rot in the second year when pathogen abundance was >log 6.0 GC g−1 root. Strain A5MH increased crop emergence and tillering biomass by up to 40%. Conclusions Further trials are required to determine if the A5MH-induced pathogen suppression translates to yield improvements in higher rainfall regions where non-cereal rotations reduce crown rot inoculum. [ABSTRACT FROM AUTHOR]

Phytophthora citrophthora and P. syringae are currently the primary causal organisms of brown rot of citrus fruits in California. To possibly find an explanation for the prevalence of the previously minor species P. syringae, we determined the population structures of both pathogens in California using next-generation sequencing and population genomics analyses. Whole-genome sequencing and aligning with newly assembled reference genomes identified 972,266 variants in 132 isolates of P. citrophthora and 422,208 variants in 154 isolates (including 24 from noncitrus tree crops) of P. syringae originating from three major growing regions. The resulting data sets were visualized using principal component analysis, discriminant analysis of principal components, unweighted pair-group method with arithmetic mean dendrograms, fastStructure, and minimum spanning networks, and we obtained the index of association, diversity summary statistics, and genetic distance statistics values GST, G′′ST, and Jost's D. Subpopulations of both species were mostly defined by their geographic origin indicating restricted dispersal of inoculum. Except for five isolates, the population structure of P. citrophthora (that is heterothallic and unlikely to reproduce sexually) was clonal to semi-clonal, with very little genetic diversity within and among subgroups. In contrast, the population structure of P. syringae was also clonal to semi-clonal, but isolates were placed into four main clusters of much higher diversity. Clonality in both species can be explained by a high level of asexual reproduction. The higher diversity in the homothallic P. syringae is likely due to commonly occurring sexual reproduction. One distinct cluster of P. syringae consisted solely of isolates from noncitrus hosts; therefore, the origin of P. syringae in citrus could not be resolved. [ABSTRACT FROM AUTHOR]

Pathogen dynamics in agroforestry systems result from several mechanisms and interactions whose independent effects are difficult to delineate. In recent decades, it has been shown that shade, as a structural feature in agroforestry systems, influences the spread of pathogens through its physical and biological effects. In Cameroon, citrus trees are mainly grown in cocoa-based agroforestry systems (CBAS), and are threatened by a variety of pathogens. This study examines how shading modifies the microclimate in the local environment of citrus trees in CBAS, and the resulting effect on citrus foot rot disease (PFRD). The study was conducted in the Cameroon agroecological zone with bimodal rainfall, where a network of 20 CBAS plots was established. Primary cartographic and structural data were used to perform static simulations with cumulative shadow overlay in ShadeMotion software. A soil sensor was used to quantify the microclimate by measuring air temperature and relative humidity above and in the soil, as well as soil pH. Relationships between shade rate, microclimatic variables, and PFRD intensity were investigated. Results showed that the effect of temperature on PFRD was independent of shade rate. A dependency relationship between relative humidity above and in the soil and PFRD according to shade rate was found. Indeed, a positive correlation of PFRD with relative humidity was observed for citrus trees located in full sunlight, while a negative correlation was observed for citrus trees located under dense and light shade. Optimization of structural characteristics of CBAS would allow ecological management of PFRD and reduction in the use of chemical pesticides. [ABSTRACT FROM AUTHOR]

BACKGROUND: SYP‐34773 is a low‐toxicity pyrimidine amine compound, which was synthesized by modifying the lead compound diflumetorim. Previous literature has shown that it can strongly inhibit the mycelial growth of several important plant pathogens, including Phytophthora litchii. However, the resistance risk of SYP‐34773 has not been reported for P. litchii. RESULTS: The mean effective concentration (EC50) value of SYP‐34773 against the mycelial growth of 111 P. litchii isolates was 0.108 ± 0.008 μg mL−1, which can be used as the baseline sensitivity for SYP‐34773 resistance detection in the future. Six mutants were obtained from two parental strain through fungicide induction, whose resistance factors fell between 194‐ and 687‐fold, with stability. Results regarding mycelial growth, sporangial production, sporangial germination, zoospore release, cystspore germination, and pathogenicity showed that the mutants' compound fitness index values were significantly lower than those of their parental isolate. Furthermore, there was no cross‐resistance between SYP‐34773 and diflumetorim in P. litchii. Significant inhibition of the mitochondrial complex I enzyme activity in two wild‐type P. litchii isolates, but not in mutants, was observed upon treatment with SYP‐34773. CONCLUSION: The resistance risk of SYP‐34773 in P. litchii is moderate, and resistance management strategies should be adopted in field use. SYP‐34773 is a mitochondrial complex I inhibitor, and SYP‐34773‐resistant P. litchii isolates did not show cross‐resistance against diflumetorim. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Context: For plant species that have evolved in fire-prone environments, declines after wildfires are often driven by the combination of fire and other threatening processes. Mitigating the impacts of these threatening processes can sometimes effectively support post-fire population recovery. Aims: We test the effectiveness of: (1) phosphite application to mitigate Phytophthora dieback; (2) fencing to exclude browsing by mammalian herbivores; and (3) translocation to sites where threats can be practically managed, for conservation of threatened flora affected by wildfires in 2018 and 2019 in the Stirling Range (Koi Kyeunu-ruff), south-western Australia. Methods: Survival of Phytophthora -susceptible flora was compared in repeatedly sampled plots from prior to and after wildfire and ± recurrent phosphite application. Survival and growth of browsing-susceptible flora was compared post-fire in fenced and control plots. Survival, growth and flowering was compared between wild populations recruiting after wildfire and translocated populations. Key results: Phosphite application increased survival of most Phytophthora -susceptible flora. Fencing led to greater growth and often increased survival. Translocated populations, with supplemental water, had greater growth rates and earlier flowering than wild populations, and a non-significant trend for higher survival. Conclusions: These findings provide strong evidence supporting continuation of phosphite application, herbivore exclusion and translocation for post-fire recovery of the threatened flora of the Stirling Range. Implications: With increasing wildfire extent, frequency and impact across the globe, successful management of non-fire threats will be crucial for post-fire conservation of threatened flora, with the approaches proving effective in this study likely to have conservation value elsewhere. Mitigation of the impacts of Phytophthora dieback and browsing by mammalian herbivores improved post-fire survival and/or growth of threatened flora in the Stirling Range (Koi Kyeunu-ruff), Western Australia. Translocated populations had greater growth and earlier flowering than wild populations. Mitigating non-fire regime threats supported post-fire recovery of threatened flora. Photographs by S. Barrett (Department of Biodiversity, Conservation and Attractions). [ABSTRACT FROM AUTHOR]