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Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

The Pseudomonas syringae species complex is a heterogeneous group of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize two P. syringae isolates collected from diseased Callery pears (Pyrus calleryana) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified the P. syringae isolates as members of phylogroup 2, related to other strains previously isolated from Pyrus and Prunus. An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2 and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole-genome sequencing of the associated phage uncovered a novel phage genus related to Pseudomonas syringae pv. actinidiae phage PHB09 and the Flaumdravirus genus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity of P. syringae and their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.IMPORTANCEGlobal change exacerbates the spread and impact of pathogens, especially in agricultural settings. There is a clear need to better monitor the spread and diversity of plant pathogens, including in potential spillover hosts, and for the development of novel and sustainable control strategies. In this study, we characterize the first described strains of Pseudomonas syringae pv. syringae isolated from Callery pear in Berkeley, California from diseased tissues in an urban environment. We show that these strains have divergent virulence profiles from previously described strains and that they can cause disease in commercial pears. Additionally, we describe a novel bacteriophage that is associated with these strains and explore its potential to act as a biocontrol agent. Together, the data presented here demonstrate that ornamental pear trees harbor novel P. syringae pv. syringae isolates that potentially pose a risk to local fruit production, or vice versa-but also provide us with novel associated phages, effective in disease mitigation.

Summary Ralstonia pseudosolanacearum, a plant pathogen responsible for bacterial wilt in numerous plant species, exhibits paradoxical growth in the host by achieving high bacterial densities in xylem sap, an environment traditionally considered nutrient‐poor. This study combined in vitro experiments and mathematical modeling to elucidate the population dynamics of R. pseudosolanacearum within plants. To simulate the xylem environment, a tomato xylem‐mimicking medium was developed. Then, a mathematical model was constructed using in vitro data and employed to simulate the dynamics of bacterial density and xylem sap composition during plant infection. The model accurately reproduced in planta experimental observations, including high bacterial densities and the depletion of glutamine and asparagine. Additionally, the model estimated the minimal number of bacteria required to initiate infection, the timing of infection post‐inoculation, the bacterial mortality rate within the plant and the rate at which bacterial putrescine is assimilated by the plant. The findings demonstrate that xylem sap can sustain high bacterial densities, provides an explanatory framework for the presence of acetate, putrescine and 3‐hydroxybutyrate in the sap of infected xylem and give clues as to the role of putrescine in the virulence of R. pseudosolanacearum. [ABSTRACT FROM AUTHOR]

Fungi of the genus Ceratocystis are aggressive tree pathogens that cause serious diseases in several crops around the world. Ceratocystis wilt disease caused by C. cacaofunesta has been shown to be responsible for severe reductions in cacao production. In this study, headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC–MS) was used in combination with chemometric analysis for monitoring volatile organic compounds (VOCs) released from C. cacaofunesta. Low-molecular-weight esters, alcohols, ketones, and sulphur compounds were identified in the liquid broth. Monitoring the volatile profile over five days of fungal growth revealed that the concentrations of alcohol and esters were inversely proportional. Acetate esters were responsible for the intense fruity aroma of the C. cacaofunesta culture produced within the first hours after fungal inoculation, which decreased over time, and are likely associated with the attraction of insect vectors to maintain the life cycle of the pathogen. PCA revealed that 3-methylbutyl acetate was the metabolite with the highest factor loading for the separation of the VOC samples after 4 h of fungal growth, whereas ethanol and 3-methylbutan-1-ol had the highest factor loadings after 96 and 120 h. 3-Methylbutan-1-ol is a phytotoxic compound that is likely associated with host cell death since C. cacaofunesta is a necrotrophic fungus. Fungal VOCs play important roles in natural habitats, regulating developmental processes and intra- and interkingdom interactions. This is the first report on the volatiles released by C. cacaofunesta. [ABSTRACT FROM AUTHOR]

BACKGROUND: Genetic improvement of crop varieties requires significant investment. Therefore, varieties must be developed to suit a broad range of breeding targets, such as yield and suitability to rainfall zones, farm management practices and quality traits. In the case of breeding for disease resistance, breeders need to consider the value of genetic improvement relative to other disease management strategies and the dynamics of pathogen genetic and phenotypic diversity. This study uses a benefit–cost analysis framework to assess the economic value of fungicide management and crop genetic improvement in disease resistance for Australian chickpea varieties. RESULTS: When assessing the likelihood of growers switching to new crop varieties with improved genetic resistance to disease, the simulation results reveal that adopting these varieties yielded higher net benefit values compared to implementing current fungicide strategies across all rainfall zones. On average, the increase in net benefit varied between 2.6% and 3.5%. Conversely, when we examined the scenario involving modifying the current fungicide strategy, we observed that, on average, switching from the current fungicide management strategy to one which involved additional fungicides was beneficial in about 73% of the cases. CONCLUSION: Our analysis reveals the importance of factors such as commodity prices, production costs, disease‐related variables and risk aversion in determining the economic benefits of adopting new crop protection strategies. Furthermore, the research reveals the need for accessible information and reliable data sources when evaluating the benefits of new agricultural technologies. This would assist growers in making informed and sustainable disease management decisions. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Introduction: Fusarium wilt, a devastating soil-borne fungal disease in flax (Linum usitatissimum), is caused by Fusarium oxysporum f. sp. lini, a hemibiotrophic plant pathogen that penetrates plant roots. There are several reports of the molecular response of L. usitatissimum to F. oxysporum f. sp. lini; however, comparisons of the effects of mutualistic and pathogenic fungi on plants are more limited. Methods: In this study, we have integrated phenotyping and RNA-Seq approaches to examine the response of flax to F. oxysporum f.sp. lini and to a mutualistic arbuscular mycorrhizal fungus (AMF) Rhizoglomus irregulare. R. irregulare is a common soil fungus and also widely used as a commercial inoculant to improve plant growth. We measured flax growth parameters after plant inoculation with each or both fungi, in comparison with non-inoculated control. We performed transcriptome analysis of root tissues collected at 9 and 14 days post-inoculation. Results: We identified several differentially expressed genes (DEGs) in response to pathogenic and mutualistic fungi. These included genes related to ethylene and salicylic acid biosynthesis, carbohydrate binding, oxidoreductases, and sugar transmembrane transporters. Genes related to calcium signaling, nutrient transport, lipid metabolism, cell wall, and polysaccharide-modifying were upregulated by R. irregulare; however, the same genes were down-regulated by F. oxysporum f. sp. lini when treated independently. In the combined treatment, genes related to cell wall modifications, hormone regulation and nutrient uptake were up-regulated. These results suggest that inoculation with R. irregulare reduced gene expression related to F. oxysporum f. sp. lini infection, leading to a reduced response to the pathogen. In response to AMF, flax prioritized mutualism-related gene expression over defense, reversing the growth inhibition caused by F. oxysporum f. sp.lini in the combined treatment. Discussion: This research provides insights into the protective effects of AMF, revealing the pre-symbiotic gene expression profile of flax in response to mutualism in comparison with pathogenicity. Potential target genes for crop improvement were identified, especially defense related genes. [ABSTRACT FROM AUTHOR]

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp-based bioinformatic analyses. Notably, homologues of Secreted in Xylem (SIX) genes, also present in many other F. oxysporum ff. spp, were identified in Fola, with both SIX9 and SIX14 (multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy of SIX8. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum ff. spp. including several in F. oxysporum f. sp. apii. Although SIX8, SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1, only SIX9 was expressed as further analysis revealed that SIX14 gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two different SIX8 sequence variants which were divergently transcribed from a shared promoter with either PSE1 or PSL1 respectively. In addition, there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed. [ABSTRACT FROM AUTHOR]

Elevation gradients strongly influence the diversity pattern of soil microorganisms. To date, many studies have elucidated the response of soil microbes to changes in elevation gradients. However, the effects of these gradients on the assembly mechanisms and network complexity of rhizospheric microbial communities remain underexplored. To bridge this knowledge gap, this study assessed the response of rhizospheric fungal communities of Pinus hwangshanensis along different elevation gradients in the Huangshan Mountain scenic area with regard to diversity, community composition, and assembly mechanisms using high-throughput amplicon sequencing. The results revealed significant differences in rhizospheric fungal community composition across three elevation gradients. The soil organic matter and pH were the most relevant factors influencing the changes in rhizospheric fungal community composition. The rhizospheric fungal diversity was significantly lower at both low and high elevations compared to the medium elevation. The rhizospheric fungal community assembly showed a more deterministic process at low and high elevations than at the medium elevation, indicating that stronger environmental filtering contributed to reduced fungal diversity at the extremes of the elevation gradient. In addition, rhizospheric pathogens, particularly Dermateaceae, acted as keystone taxa, diminishing the stability of co-occurrence networks at the medium elevation. This study contributes to a more comprehensive understanding of rhizospheric fungal community patterns and their ecological functions along elevation gradients in mountainous regions. [ABSTRACT FROM AUTHOR]

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Colletotrichum gloeosporioides (Cg), Pestalotiopsis sp. (Ps), Fusarium oxysporum (Fo), and Fusarium proliferatum (Fp) are pathogens that cause various diseases of Cymbidium kanran. Species identification based on the morphological characteristics of pathogen-infected orchids is very complex and difficult; therefore, specific and reliable diagnostic methods are needed. Here, we developed a multiplex polymerase chain reaction (PCR) assay for simultaneous detection of Cg, Ps, Fo, and Fp. Four pairs of pathogen-specific primers were designed based on the internal transcribed spacer sequences of each pathogen, generating fragments of 480, 407, 321, and 279 bp, respectively. The multiplex PCR assay using these four pairs of mixed primers effectively detected the four pathogens simultaneously, with a sensitivity of 0.1 ng genomic DNA/pathogen. Application of the optimized multiplex PCR assay to symptomatic C. kanran leaf samples effectively detected single or multiple pathogens. These results indicate that the multiplex PCR developed in this study is not only a rapid and reliable method for detecting four problematic pathogens in C. kanran, but also serves as a very useful tool for early diagnosis.

KRS022 was isolated from the rhizosphere soil of a healthy plant in a pathogen-infested cotton field in Xinjiang, China. Previous studies have demonstrated that KRS022 possesses the ability to trigger plant immune responses, inhibit the growth of various pathogenic fungi, including Verticillium dahliae, and promote plant growth. The antagonistic properties of KRS022 primarily stem from its bioactive metabolites. In this study, the high-quality genome of KRS022 was obtained. The KRS022 genome consists of a chromosome of 6,369,026 bp with 67.09% GC content and possesses 5,830 open reading frames, of which 5,186 genes were annotated, and 119 were ncRNA genes. Additionally, 11 gene clusters of secondary metabolites biosynthesis were predicted, involved in polyketide synthase, arylpolyene, NAGGN, beta-lactone, ranthipeptide, PiPP-like, redox cofactor, and non-ribosomal peptide-synthetase clusters. It could be useful to explore the biocontrol potential of P. tohonis, implying promising application of KRS022 to biological control. [Figure: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant–microbe-microbe interactions on the leaf surface.

Late leaf spot of groundnut is caused by the fungal pathogen of Cercosporidium personatum. Efforts to prevent this disease generally use synthetic fungicides that can cause environmental pollution. This study aims to identify the fungal pathogen of groundnut late leaf spot and study the antifungal effect of leaf extract of some plants for leaf spot intensity suppression. Late leaf spot pathogen was identified based on morphological characteristics of hyphae and conidia. The leaf extracts of butterfly pea (Clitoria ternatea), Mexican sunflower (Tithonia diversifolia), basil (Ocimum gratissimum), and sugar apple (Annona squamosa) at a concentration of 25% against C. personatum were evaluated in vitro based on growth inhibition. The growth and intensity of groundnut disease attacks were assessed for seven weeks by inoculating C. personatum and application of the leaf extracts. Results showed that the pathogen was identified as C. personatum with conidia characteristics of cylindrical to obclavate, short and slightly curved with four septa, and 35.75 × 7.11 µm in size. The percentage of inhibition of C. personatum in vitro reached 94.03% by leaf extract of C. ternatea, 88.56% by T. diversifolia, 87.20% by O. gratissimum, and 84.10% by A. squamosa. Treatment of C. ternatea increased plant height up to 12.85% and reduced the most optimal percentage of the infected leaves up to 61.53%. C. ternatea leaf extract was found to be the most effective extract to suppress C. personatum infection by 77.94%, while T. diversifolia, O. gratissimum, and A. squamosa reduced disease severity by 70.15%, 65.43%, and 57.76%, respectively.

This study investigates the histidine kinase (HK) gene repertoire of Enterobacter hormaechei strain HCF3, isolated from fresh cow dung in Mogosane Village, Northwest Province, South Africa. Histidine kinases are critical components of bacterial two-component signal transduction systems, enabling bacteria to sense and adapt to diverse environmental conditions. Given the growing concern over antimicrobial resistance (AMR) associated with E. hormaechei, this research elucidates the genetic components that facilitate its environmental adaptability. After isolating the strain, genomic sequencing using Illumina technology, resulting in high-quality sequence data, was conducted. The assembled genome was meticulously annotated and deposited in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA991313, with additional accession numbers for raw reads (JAUOLV000000000.1) and BioSample (SAMN36292742). Histidine kinase genes were identified based on conserved domains, particularly HisKA and HATPase. This led to compiling a comprehensive HK gene catalogue with locus tags, protein accession numbers, and functional annotations. To validate the HK gene set of E. hormaechei HCF3, we conducted a rigorous comparative analysis with other strains. This revealed that strain HCF1 contains 21 histidine kinase genes, HCF2 has 25, while HCF4 has 19. These findings underscore the diversity and conservation of HK genes across different Enterobacter species, providing a new perspective on their evolutionary significance. The assembled dataset provides valuable insights into the signalling pathways of E. hormaechei, highlighting the potential roles of HKs in environmental sensing, adaptation, and pathogenicity. Furthermore, this research lays the groundwork for future studies on the applications of these genes in agriculture and biotechnology, offering new avenues for understanding and managing E. hormaechei in various ecological contexts.

A novel species of Mucor was identified as the causal agent of a brown rot of Prunus domestica (European plum), widely grown in the south of Xinjiang, China. This disease first appears as red spots after the onset of the fruits. With favorable environmental conditions, fruit with infected spots turn brown, sag, expand, wrinkle, and harden, resulting in fruit falling. Fungal species were isolated from infected fruits. A phylogenetic analysis based on internal transcribed spacer (ITS) regions and the large subunit (LSU) of the nuclear ribosomal RNA (rRNA) gene regions strongly supported that these isolates made a distinct evolutionary lineage in Mucor (Mucoromycetes, Mucoraceae) that represents a new taxonomic species, herein named as Mucor xinjiangensis. Microscopic characters confirmed that these strains were morphologically distinct from known Mucor species. The pathogenicity of M. xinjiangensis was confirmed by attaching an agar disk containing mycelium on fruits and re-isolation of the pathogen from symptomatic tissues. Later, fourteen fungicides were selected to determine the inhibitory effect on the pathogen. Further, results showed that difenoconazole had the best effect on the pathogen and the strongest toxicity with the smallest half maximal effective concentration (EC50) value, followed by a compound fungicide composed of difenoconazole with azoxystrobin, mancozeb, prochloraz with iprodione, pyraclostrobin with tebuconazole, and trifloxystrobin with tebuconazole and ethhylicin. Present study provides the basis for the prevention and control of the novel plum disease and its pathogen. [ABSTRACT FROM AUTHOR]

The pathogen Agrobacterium tumefaciens is known for causing crown gall tumours in plants. However, it has also been harnessed as a valuable tool for plant genetic transformation. Apart from the T‐DNA, Agrobacterium also delivers at least five virulence proteins into the host plant cells, which are required for an efficient infection. One of these virulence proteins is VirD5. F‐box proteins, encoded in the host plant genome or the Ti plasmid, and the ubiquitin/26S proteasome system (UPS) also play an important role in facilitating Agrobacterium infection. Our study identified two Arabidopsis F‐box proteins, D5BF1 and D5BF2, that bind VirD5 and facilitate its degradation via the UPS. Additionally, we found that Agrobacterium partially suppresses the expression of D5BF1 and D5BF2. Lastly, stable transformation and tumorigenesis efficiency assays revealed that D5BF1 and D5BF2 negatively regulate the Agrobacterium infection process, showing that the plant F‐box proteins and UPS play a role in defending against Agrobacterium infection. [ABSTRACT FROM AUTHOR]

Weeds are one of the most serious pests to agricultural production, and their control mainly depends on chemical herbicides. Long-term and large-scale use of chemical herbicides will lead to the increase of weed resistance, environmental security and food security. Microbial herbicides are biological herbicides developed by using microorganisms themselves or their metabolites, which are characterized by abundant resources, environmental friendliness, not easy to have resistant weeds, which are the development direction of green weed biocontrol in the world. In this paper, we summarized the types of microbial herbicides and listed the biocontrol microorganisms and toxins with herbicidal activity. Then, we reviewed the mechanism of microbial weed control. Microorganisms invaded the weed host through infection, causing the tube closure of the weed, and finally resulting in plant wilting and dying. In otherwise, they affected the cell structure integrity, biofilm function, lipid stability, energy transfer, photosynthetic pigment synthesis, lipid synthesis and amino acid synthesis of the weed host through effective active substances in metabolites, to achieve the purpose of killing weeds. In addition, we summarized the application status of microbial herbicides, including commercialization, constraints in application and improvement strategies of control effect; as well as the application of omics technology in the field of microbial herbicides. Finally, we prospected the development direction and application prospect of microbial herbicides，aiming to provide reference for the research and development of new herbicides. [ABSTRACT FROM AUTHOR]

Outbreaks of insects and diseases are part of the natural disturbance regime of all forests. However, introduced pathogens have had outsized impacts on many dominant forest tree species over the past century. Mitigating these impacts and restoring these species are dilemmas of the modern era. Here, we review the ecological and economic impact of introduced pathogens, focusing on examples in North America. We then synthesize the successes and challenges of past biotechnological approaches and discuss the integration of genomics and biotechnology to help mitigate the effects of past and future pathogen invasions. These questions are considered in the context of the transgenic American chestnut, which is the most comprehensive example to date of how biotechnological tools have been used to address the impacts of introduced pathogens on naïve forest ecosystems. [ABSTRACT FROM AUTHOR]

The presence of bacteria belonging to the Pseudomonas syringae complex in the natural vegetation of several Icelandic habitat types has been recently reported, raising questions about the risk to Icelandic crops, particularly given the expected increase in agricultural activity due to climate warming. This study takes advantage of Iceland's unique characteristics and the discovery of P. syringae in Peltigera lichens to gain a better understanding of the potential risk posed by this newly discovered ecological niche. The main objective was to evaluate the pathogenic potential and fitness in crops of P. syringae strains isolated from Peltigera lichen sampled in Iceland, focusing on strains that belong to phylogroups 1 and 2, which commonly contain epidemic strains. The results indicate that P. syringae strains isolated from Icelandic Peltigera lichen have a comparable fitness to epidemic strains in 8 out of 10 tested plant species (rice, tomato, thale cress, annual mugwort, spinach, garlic chives, tobacco and kale). Furthermore, pathogenicity assessment on three plant species highlighted that certain strains also caused similar symptoms and disease severity compared to epidemic strains. These findings provide valuable insights into the potential risks posed by P. syringae from Icelandic natural habitats and illustrate how strains from these habitats have a wide pathogenic potential to crops without having encountered these crops in the last several thousand years of their presence in Iceland. [ABSTRACT FROM AUTHOR]

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant–microbe-microbe interactions on the leaf surface. [ABSTRACT FROM AUTHOR]

In recent years, the production and demand of berries in the world have gradually increased, but the infection of fungal pathogens has become one of the important factors restricting the production and sales of fresh berries. It has been found that Alternaria can cause a variety of plant diseases and fruit rot worldwide. This review introduces the effect of Alternaria infection on berry quality, including physical, chemical and physiological aspects, and discusses the possible infection mechanisms. In addition, Alternaria produces toxins during infections and seriously threatens the safety of berries and consumer health. Therefore, the prevention and control measures of Alternaria are systematically summarized. This review provides the basis for further optimization of postharvest preservation technology and fruit quality, to prolong the shelf life of berries. We can realistically expect to control plant diseases with increasing efficiency, which is conducive to improving the quality and safety of postharvest berry fruits. [ABSTRACT FROM AUTHOR]

To cause disease in plants, pathogens not only require a susceptible host, but also often require specific environmental conditions suitable for pathogenesis. Multiple aspects of climate are predicted to change dramatically over the coming decades, which will result in increases in CO 2 and, depending on location, temperature, humidity, salinity, flooding, or drought. Climate change will result in increases in the prevalence, dispersal, and range of different plant pathogens, while simultaneously affecting the virulence mechanisms of microbial pathogens. The plant immune system can be compromised by extremes in climatic conditions and crosstalk with abiotic stress signaling pathways. Several recent reports have unraveled how climatic factors affect plants at the molecular level, raising the possibility of modifying these pathways for climate-smart, pathogen-resistant crops. Variations in climate conditions can dramatically affect plant health and the generation of climate-resilient crops is imperative to food security. In addition to directly affecting plants, it is predicted that more severe climate conditions will also result in greater biotic stresses. Recent studies have identified climate-sensitive molecular pathways that can result in plants being more susceptible to infection under unfavorable conditions. Here, we review how expected changes in climate will impact plant–pathogen interactions, with a focus on mechanisms regulating plant immunity and microbial virulence strategies. We highlight the complex interactions between abiotic and biotic stresses with the goal of identifying components and/or pathways that are promising targets for genetic engineering to enhance adaptation and strengthen resilience in dynamically changing environments. [ABSTRACT FROM AUTHOR]

This article explores the use of metagenomics in studying plant diseases and understanding microbial communities. It discusses the challenges of traditional methods and the benefits of metagenomics in uncovering the diversity and composition of plant-associated microbiomes. The article provides best practices for generating metagenomic workflows and emphasizes the importance of experimental design and sequencing rationale. It also discusses the use of different sequencing technologies and the need for proper databases in classifying metagenomic data. The document includes a list of references and a glossary of terms related to plant science and microbiology, which can be helpful for researchers studying plant diseases and genetic diversity in plants. [Extracted from the article]

Dickeya dadantii is a common pathogen of bacterial soft rot on a wide range of plants, including several crops. In this study, we present the complete genome sequence of the D. dadantii type strain DSM18020T. The genome was assembled using PacBio technology, resulting in a 4,997,541 bp circular chromosome with a G+C content of 56.5%. Our sequence analyses predicted 4277 protein-encoding genes, including several associated with known bacterial virulence factors and secondary metabolites. Comparative genomics analysis between Dickeya revealed that the category of 'metabolism' is the most important in both the core and accessory genomes, while the category of 'information storage and processing' is the most dominant in unique genomes. These findings will not only help us to understand the pathogenic mechanisms of D. dadantii DSM18020T, but also provide us with useful information for new control strategies against this phytopathogen. [ABSTRACT FROM AUTHOR]

The fungarium was collected by Jerzy Wojciech Szulczewski in the Wielkopolska region in Western Poland in 1909–1911, 1928, and 1960–1966 (nine volumes). It includes dried plant specimens with disease symptoms of fungal origin and is currently located in the POZ Herbarium (Adam Mickiewicz University, Poznań, Poland). It is one of the oldest and richest Polish collections of this category although some parts were destroyed or lost after the Second World War. Many of the sheets have original annotations by the author and hand-written labels with both plant and fungus names. A checklist of all species is presented in the appendix. The whole collection was digitized in 2023 and is available on the website of the AMUNATCOLL project. [ABSTRACT FROM AUTHOR]

The phytopathogenic genus, Entomosporium can cause serious leaf diseases worldwide. Entomosporium has long been regarded as a synonym of Diplocarpon. However, different morphologies between Entomosporium and Diplocarpon make this doubtful. Based on morpho-phylogenetic analyses, the placement of the genus was re-evaluated in this study. The combined the internal transcribed spacer gene region (ITS) and the 28S large subunit ribosomal RNA gene region (LSU) phylogenetic analysis shows that Entomosporium is an independent clade within Drepanopezizaceae and formed a sister clade to the generic type Diplocarpon. Moreover, Hymenula and Pseudopeziza do not cluster in Drepanopezizaceae. We propose to resurrect the name Entomosporium, and exclude Hymenula cerealis and Pseudopeziza medicaginis from Drepanopezizaceae and propose to treat them under Ploettnerulaceae. A new species, E. dichotomanthes is also introduced from China based on morpho-molecular analyses which is associated with Dichotomanthes tristaniicarpa. [ABSTRACT FROM AUTHOR]

Chemical fungicides have been widely used to control plant diseases caused by fungal pathogens. Still, the overuse of these fungicides has led to concerns about the hazards to humans, animals, and the environment and an increase in fungicide resistance. Interest in biocontrol agents with strong antimicrobial activity has significantly increased to counteract the escalating risks of chemical fungicides. Our previous study found that a soil-born microbe, Brevibacillus brevis HK544, exhibited a promising antifungal activity against a plant pathogen, Fusarium graminearum, with edeine B1 identified as the active compound. Herein, we extended our study to investigate the in vitro and in vivo antifungal spectrum of B. brevis HK544, including edeine B1, against various plant pathogenic fungi and evaluated the possibility that B. brevis HK544 could be used in combination with chemical fungicides to enhance the disease control efficacy. With an in vitro broad-spectrum antifungal activity, the B. brevis HK544 culture filtrate, culture broth, and metabolite edeine B1 exhibited a promising disease control efficacy against tomato gray mold and tomato late blight among the tested fungal diseases. Based on the in vitro antifungal activity against Botrytis cinerea, when edeine B1 was combined with various chemical fungicides, the highest average synergy score among the tested combinations was observed in the edeine B1 and benomyl combination. The co-application of the B. brevis HK544 culture filtrate and benomyl improved the disease control efficacy against gray mold disease, supporting the in vitro result. Taken together, our results show that B. brevis HK544 has potential as a biological control agent for controlling plant pathogenic fungi and also that B. brevis HK544 could be combined with chemical fungicides to enhance the efficacy of antifungal agents.

IntroductionFusarium wilt, a devastating soil-borne fungal disease in flax (Linum usitatissimum), is caused by Fusarium oxysporum f. sp. lini, a hemibiotrophic plant pathogen that penetrates plant roots. There are several reports of the molecular response of L. usitatissimum to F. oxysporum f. sp. lini; however, comparisons of the effects of mutualistic and pathogenic fungi on plants are more limited.MethodsIn this study, we have integrated phenotyping and RNA-Seq approaches to examine the response of flax to F. oxysporum f.sp. lini and to a mutualistic arbuscular mycorrhizal fungus (AMF) Rhizoglomus irregulare. R. irregulare is a common soil fungus and also widely used as a commercial inoculant to improve plant growth. We measured flax growth parameters after plant inoculation with each or both fungi, in comparison with non-inoculated control. We performed transcriptome analysis of root tissues collected at 9 and 14 days post-inoculation.ResultsWe identified several differentially expressed genes (DEGs) in response to pathogenic and mutualistic fungi. These included genes related to ethylene and salicylic acid biosynthesis, carbohydrate binding, oxidoreductases, and sugar transmembrane transporters. Genes related to calcium signaling, nutrient transport, lipid metabolism, cell wall, and polysaccharide-modifying were up-regulated by R. irregulare; however, the same genes were down-regulated by F. oxysporum f. sp. lini when treated independently. In the combined treatment, genes related to cell wall modifications, hormone regulation and nutrient uptake were up-regulated. These results suggest that inoculation with R. irregulare reduced gene expression related to F. oxysporum f. sp. lini infection, leading to a reduced response to the pathogen. In response to AMF, flax prioritized mutualism-related gene expression over defense, reversing the growth inhibition caused by F. oxysporum f. sp.lini in the combined treatment.DiscussionThis research provides insights into the protective effects of AMF, revealing the pre-symbiotic gene expression profile of flax in response to mutualism in comparison with pathogenicity. Potential target genes for crop improvement were identified, especially defense related genes.

High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.

We induced immune activation in mass rearing experiments in three insect species, i.e., Gryllus bimaculatus De Geer, 1773 (Orthoptera: Gryllidae), Hermetia illucens (Linnaeus, 1758) (Diptera: Stratiomyidae), and Protaetia brevitarsis seulensis (Kolbe, 1886) (Coleoptera: Scarabaeidae). Lysosomal staining of immune cells was a little over 6% in the control group insects, whereas it ranged from 17-35% in insects immunized with Escherichia coli K12 or Bacillus thuringiensis (Bt). The expression of attacin-like protein and defensin-like protein was also found to be upregulated at least 10-fold, and even up to 30-fold, from the third day of rearing in insects immunized with E. coli K12 or Bt. Non-immunized or immunized G. bimaculatus, H. illucens, and P. brevitarsis seulensis were freeze-dried and powdered, and these powders were then tested for protection against Pectobacterium carotovorum infestation. No inhibitory effects on P. carotovorum were observed when using all non-immunized insect powders or PBS. However, in the clear zone test treated with H. illucens powder at 10,000 ppm, an average size of 21.67 mm was observed. In a test using potato slices infected with P. carotovorum, we observed severe disease occurrence and potato weight loss in all non-immunized insect powders or PBS-treated groups. However, the group treated with H. illucens powder had the least potato weight loss. When tested on lettuce, the H. illucens powder-treated group revealed an approximately 10% increase in the fresh weight of lettuce, with both the dry weight and leaf area of lettuce increasing in comparison with those in the control group. Thus, our study proposes a novel method for the use of freeze-dried and powdered forms of insects immunized in mass rearing as effective functional fertilizers on a large scale that can also be effective in inhibiting microbial infections, overcoming the limitation of high production costs of such insect fertilizers using conventional methods.

Abstract Puccinia abrupta var. partheniicola, the so-called winter rust of parthenium weed (Parthenium hysterophorus), an invasive alien weed in India, was rediscovered at an epiphytotic scale in February 2023 following a prolonged period of presumed absence in the field. Disease incidence was 80–90% in large tracts of P. hysterophorus stands along the roadsides in an area of 5 km2 near Attibele–Sarjapura road (948A) in Anekal taluk of Bengaluru Urban district in Karnataka. Pycnial, aecial or telial stages of the rust were not found. The morphological parameters of uredinia and urediniospores completely matched those originally described, thus confirming the fungal identity. The significance of this rust epiphytotic to P. hysterophorus biocontrol in India is discussed together with the planned follow-up activities.

Abstract Background The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. Results The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. Conclusions This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen’s life cycle and a solid foundation for studying EFB.

The Namib Desert (Namibia) is home to fairy circles which are barren, circular to almost-circular patches of land surrounded by grasses. During a survey of the fungi associated with the most common grass species, Stipagrostis ciliata (Poaceae), and its rhizospheric soils associated with these fairy circles, Curvularia was commonly isolated (80 strains). Curvularia is a cosmopolitan fungal genus that occurs in diverse geographical locations and on a wide range of substrates, but particularly on foliar plants. Curvularia strains were identified based on multilocus sequence comparisons of their internal transcribed spacer rDNA region (ITS), and the partial gene regions of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and translation elongation factor 1-alpha (TEF1). The strains belonged to 13 species, including the discovery of five novel Curvularia species. The aim of this paper was to report on the identified species and to formally describe and name the new species as C. deserticola, C. gobabebensis, C. maraisii, C. namibensis, and C. stipagrostidicola. [ABSTRACT FROM AUTHOR]

Fraxinus ornus and F. excelsior are naturally occurring woodland trees and widely cultivated ornamental plants in Hungary. Leaves with powdery mildew symptoms observed unusually on adaxial side of leaves of F. ornus and F. excelsior were collected from two locations in Hungary. We identified the causing fungi based on their morphological characteristics and molecular phylogenetic analysis. Numerous chasmothecia were found on a part of the samples, which were spherical, 83–120 µm in diameter, and the apices of the appendages uncinated or spirally curved. Anamorphs were characterized by conidiophores developing conidia singly, and by hyphae with lobed appressoria, characteristic of Erysiphe spp. The internal transcribed spacer region of the nrDNA was amplified, and the BLAST searches showed 100% similarity with Erysiphe salmonii sequences in GenBank. In the phylogenetic analysis the sequences of the Hungarian samples grouped in one clade with the sequences of other E. salmonii specimens collected in Central and Eastern Europe and Asia. This is the first report of the non-native E. salmonii causing powdery mildew on Fraxinus sp. in Hungary. [ABSTRACT FROM AUTHOR]

Species of Pseudocercospora are commonly associated with leaf and fruit spots on diverse plant hosts in sub-tropical and tropical regions. Pseudocercospora spp. have mycosphaerella-like sexual morphs, but represent a distinct genus in Mycosphaerellaceae (Mycosphaerellales, Dothideomycetes). The present study adds a further 29 novel species of Pseudocercospora from 413 host species representing 297 host genera occurring in 60 countries and designates four epitypes and one lectotype for established names. This study recognises 329 species names, with an additional 69 phylogenetic lineages remaining unnamed due to difficulty in being able to unambiguously apply existing names to those lineages. To help elucidate the taxonomy of these species, a phylogenetic tree was generated from multi-locus DNA sequence data of the internal transcribed spacers and intervening 5.8S nuclear nrRNA gene (ITS), partial actin (actA), and partial translation elongation factor 1-alpha (tef1), as well as the partial DNA-directed RNA polymerase II second largest subunit (rpb2) gene sequences. Novel species described in this study include those from various countries as follows: Australia, Ps. acaciicola from leaf spots on Acacia sp., Ps. anopter from leaf spots on Anopterus glandulosus, Ps. asplenii from leaf spots on Asplenium dimorphum, Ps. australiensis from leaf spots on Eucalyptus gunnii, Ps. badjensis from leaf spots on Eucalyptus badjensis, Ps. erythrophloeicola from leaf spots on Erythrophleum chlorostachys, Ps. grevilleae from leaf spots on Grevillea sp., Ps. lophostemonigena from leaf spots on Lophostemon confertus, Ps. lophostemonis from leaf spots on Lophostemon lactifluus, Ps. paramacadamiae from leaf spots on Macadamia integrifolia, Ps. persooniae from leaf spots on Persoonia sp., Ps. pultenaeae from leaf spots on Pultenaea daphnoides, Ps. tristaniopsidis from leaf spots on Tristaniopsis collina, Ps. victoriae from leaf spots on Eucalyptus globoidea. Brazil, Ps. musigena from leaf spots on Musa sp. China, Ps. lonicerae-japonicae from leaf spots on Lonicera japonica, Ps. rubigena leaf spots on Rubus sp. France (Réunion), Ps. wingfieldii from leaf spots on Acacia heterophylla. Malaysia, Ps. musarum from leaf spots on Musa sp. Netherlands, Ps. rhododendri from leaf spots on Rhododendron sp. South Africa, Ps. balanitis from leaf spots on Balanites sp., Ps. dovyalidicola from leaf spots on Dovyalis zeyheri, Ps. encephalarticola from leaf spots on Encephalartos sp. South Korea, Ps. grewiana from leaf spots on Grewia biloba, Ps. parakaki from leaf spots on Diospyros kaki, Ps. pseudocydoniae from leaf spots on Chaenomeles lagenaria, Ps. paracydoniae from leaf spots on Chaenomeles speciosa. Thailand, Ps. acerigena from leaf spots on Acer sp., Ps. tectonigena from leaf spots on Tectona grandis. Epitypes are designated for Cercospora bonjeaneae-rectae, Cercospora halleriae, Ps. eucleae, and an epitype as well as a lectotype for Ps. macadamiae. Results obtained in the present study contribute to a better understanding of the host specificity and distribution in Pseudocercospora spp., many of which represent important pathogens of food or fibre crops, or organisms of quarantine concern. [ABSTRACT FROM AUTHOR]

Streptomyces have a uniquely complex developmental life cycle that involves the coordination of morphological differentiation with the production of numerous bioactive specialized metabolites. The majority of Streptomyces spp. are soil-dwelling saprophytes, while plant pathogenicity is a rare attribute among members of this genus. Phytopathogenic Streptomyces are responsible for economically important diseases such as common scab, which affects potato and other root crops. Following the acquisition of genes encoding virulence factors, Streptomyces pathogens are expected to have specifically adapted their regulatory pathways to enable transition from a primarily saprophytic to a pathogenic lifestyle. Investigations of the regulation of pathogenesis have primarily focused on Streptomyces scabiei and the principal pathogenicity determinant thaxtomin A. The coordination of growth and thaxtomin A production in this species is controlled in a hierarchical manner by cluster-situated regulators, pleiotropic regulators, signalling and plant-derived molecules, and nutrients. Although the majority of phytopathogenic Streptomyces produce thaxtomins, many also produce additional virulence factors, and there are scab-causing pathogens that do not produce thaxtomins. The development of effective control strategies for common scab and other Streptomyces plant diseases requires a more in-depth understanding of the genetic and environmental factors that modulate the plant pathogenic lifestyle of these organisms. [ABSTRACT FROM AUTHOR]

Chickpea (Cicer arietinum) is a major food legume providing high quality nutrition, especially in developing regions. Chickpea wilt (Fusarium oxysporum f. sp. ciceris) causes significant annual losses. Integrated disease management of Fusarium wilt is supported by resistant varieties. Relatively few resistance genes are known so there is value in exploring genetic resources in chickpea wild relatives. This study investigates the inheritance of Fusarium wilt resistance (race 2) in recombinant inbred lines (RILs) from a cross between a cultivated susceptible chickpea variety (Gokce) and a wild resistant Cicer reticulatum line (Kayat-077). RILs, parents, resistant and susceptible tester lines were twice grown in the greenhouse with inoculation and disease symptoms scored. DNA was extracted from dried leaves and individuals were single nucleotide polymorphism (SNP) genotyped. SNPs were placed on the reference chickpea genome and quantitative trait locus (QTL) mapping was performed. Significant QTL regions were examined using PulseDB to identify candidate genes. The results showed the segregation of Fusarium wilt resistance conforming to a single gene inheritance. One significant QTL was found at the start of chromosome 8, containing 138 genes, three of which were disease-resistance candidates for chickpea breeding. [ABSTRACT FROM AUTHOR]

Phenology is a key adaptive trait of organisms, shaping biotic interactions in response to the environment. It has emerged as a critical topic with implications for societal and economic concerns due to the effects of climate change on species' phenological patterns. Fungi play essential roles in ecosystems, and plant pathogenic fungi have significant impacts on global food security. However, the phenology of plant pathogenic fungi, which form a huge and diverse clade of organisms, has received limited attention in the literature. This diversity may have limited the use of a common language for comparisons and the integration of phenological data for these taxonomic groups. Here, we delve into the concept of 'phenology' as applied to plant pathogenic fungi and explore the potential drivers of their phenology, including environmental factors and the host plant. We present the PhenoFun scale, a phenological scoring system suitable for use with all fungi and fungus‐like plant pathogens. It offers a standardised and common tool for scientists studying the presence, absence, or predominance of a particular phase, the speed of phenological phase succession, and the synchronism shift between pathogenic fungi and their host plants, across a wide range of environments and ecosystems. The application of the concept of 'phenology' to plant pathogenic fungi and the use of a phenological scoring system involves focusing on the interacting processes between the pathogenic fungi, their hosts, and their biological, physical, and chemical environment, occurring during the life cycle of the pathogen. The goal is to deconstruct the processes involved according to a pattern orchestrated by the fungus's phenology. Such an approach will improve our understanding of the ecology and evolution of such organisms, help to understand and anticipate plant disease epidemics and their future evolution, and make it possible to optimise management models, and to encourage the adoption of cropping practices designed from this phenological perspective. [ABSTRACT FROM AUTHOR]

In this case study, the current situation faced by coffee growers attempting to control coffee leaf rust (Hemileia vastatrix) in Hawaii is reported. CLR is considered the most devastating disease affecting coffee crops worldwide and was detected in Hawaii in 2020. Three small coffee farms from the South Kona district of Hawaii Island were selected. The goals of this case study were to: (1) assist coffee growers in the early detection of CLR incidence, and consequently support farmers with recommendations for control, (2) record agronomic information and management practices, and (3) estimate the cost to control CLR during 2021 and 2022 seasons. Low CLR incidence (<4%) was initially observed at all farms (January–June 2021), but increased as the harvest began, ending the season (December 2021) at 77%, 21% and 6% incidence at farms 1, 2 and 3, respectively. At the end of 2022 season (December), CLR incidence reached 43%, 20% and 3% at farms 1, 2 and 3, respectively. The number of sprays per season (5–10), the type of fungicides applied (preventive, curative), the timing of sprays, the efficacy of applications and weather conditions all played a role in determining the infection rates at each farm. Effective control of CLR is possible in Hawaii if the sprays of fungicides are carried out with the right products, appropriate timing and good coverage. [ABSTRACT FROM AUTHOR]

For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6–10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases. [ABSTRACT FROM AUTHOR]

Introduction: Pectobacterium betavasculorum is a member of the Pectobacerium genus that inhabits a variety of niches and is found in all climates. Bacteria from the Pectobacterium genus can cause soft rot disease on various plants due to the secretion of plant cell wall degrading enzymes (PCWDEs). The species P. betavasculorum is responsible for the vascular necrosis of sugar beet and soft rot of many vegetables. It also infects sunflowers and artichokes. The main sugar present in sugar beet is sucrose while xylose is one of the main sugars in artichoke and sunflower. Methods: In our work, we applied metabolomic studies coupled with genomics to investigate the metabolism of P. betavasculorum in the presence of xylose and sucrose as the only carbon source. The ability of the strains to use various sugars as the only carbon source were confirmed by the polypyridyl complex of Ru(II) method in 96-well plates. Results: Our studies provided information on the metabolic pathways active during the degradation of those substrates. It was observed that different metabolic pathways are upregulated in the presence of xylose in comparison to sucrose. Discussion: The presence of xylose enhances extracellular metabolism of sugars and glycerol as well as stimulates EPS and IPS synthesis. In contrast, in the presence of sucrose the intensive extracellular metabolism of amines and amino acids is promoted. [ABSTRACT FROM AUTHOR]

Fruits and vegetables are an integral part of our diet attributed to their appealing taste, flavor, and health-promoting characteristics. However, due to their high-water activity, they are susceptible to microbial spoilage and diseases at any step in the food supply chain, from pre-harvest treatment to post-harvest storage and transportation. As a result, food researchers and engineers are developing innovative technologies that can be used to reduce the loss of fruits and vegetables on-farm and during postharvest processing. The purpose of this study was to gather and discuss the scientific data on the disease-suppressive activity of nanoparticles against plant pathogens. The progress and limitations of innovative approaches for improving nanoparticles' efficiency and dependability have been studied to develop effective substitutes for synthetic chemical fungicides and pesticides, in managing disease in fruits and vegetables. The findings of this study strongly suggests that nanotechnology has the required ability for disease suppression in fruits and vegetables. Applications of specific nanoparticles under specified conditions can enhance nutrition delivery to plants, provide better antibacterial and disease suppression activity. Nanoparticles can also lessen the quantity of agrichemicals/metals released into the environment as compared to standard formulations, which is one of the most impressive advances. [ABSTRACT FROM AUTHOR]

The rate and trajectory of evolution in an obligate parasite is critically dependent on those of its host(s). Adaptation to a genetically homogeneous host population should theoretically result in specialization, while adaptation to an evolving host population (i.e., coevolution) can result in various outcomes including diversification, range expansion, and/or local adaptation. For viruses of bacteria (bacteriophages, or phages), our understanding of how evolutionary history of the bacterial host(s) impacts viral genotypic and phenotypic evolution is currently limited. In this study, we used whole genome sequencing and two different metrics of phage impacts to compare the genotypes and phenotypes of lytic phages that had either coevolved with or were repeatedly passaged on an unchanging (ancestral) strain of the phytopathogen Pseudomonas syringae. Genomes of coevolved phages had more mutations than those of phages passaged on a constant host, and most mutations were in genes encoding phage tail‐associated proteins. Phages from both passaging treatments shared some phenotypic outcomes, including range expansion and divergence across replicate populations, but coevolved phages were more efficient at reducing population growth (particularly of sympatric coevolved hosts). Genotypic similarity correlated with infectivity profile similarity in coevolved phages, but not in phages passaged on the ancestral host. Overall, while adaptation to either host type (coevolving or ancestral) led to divergence in phage tail proteins and infectivity patterns, coevolution led to more rapid molecular changes that increased bacterial killing efficiency and had more predictable effects on infectivity range. Together, these results underscore the important role of hosts in driving viral evolution and in shaping the genotype–phenotype relationship. [ABSTRACT FROM AUTHOR]

Powdery mildew is one of the most problematic diseases in strawberry production. To date, few commercial strawberry cultivars are deemed to have complete resistance and as such, an extensive spray programme must be implemented to control the pathogen. Here, a large-scale field experiment was used to determine the powdery mildew resistance status of leaf and fruit tissues across a diverse panel of strawberry genotypes. This phenotypic data was used to identify Quantitative Trait Nucleotides (QTN) associated with tissue- specific powdery mildew resistance. In total, six stable QTN were found to be associated with foliar resistance, with one QTN on chromosome 7D associated with a 61% increase in resistance. In contrast to the foliage results, there were no QTN associated with fruit disease resistance and there was a high level of resistance observed on strawberry fruit, with no genetic correlation observed between fruit and foliar symptoms, indicating a tissue-specific response. Beyond the identification of genetic loci, we also demonstrate that genomic selection can lead to rapid gains in foliar resistance across genotypes, with the potential to capture >50% of the genetic foliage resistance present in the population. To date, breeding of robust powdery mildew resistance in strawberry has been impeded by the quantitative nature of natural resistance and a lack of knowledge relating to the genetic control of the trait. These results address this shortfall, through providing the community with a wealth of information that could be utilized for genomic informed breeding, implementation of which could deliver a natural resistance strategy for combatting powdery mildew. [ABSTRACT FROM AUTHOR]

Kauri (Agathis australis), a tree species endemic to northern New Zealand, is threatened by kauri dieback disease, caused by the plant pathogen Phytophthora agathidicida. Some human and animal activities capable of disturbing and transferring infected soil may facilitate the spread of this pathogen. Feral pigs (Sus scrofa) are thought to be especially important due to their foraging behaviour. Consequently, management of feral pigs has been proposed as a key mitigation strategy for reducing the impacts of kauri dieback disease. We reviewed the evidence for feral pigs facilitating the spread of P. agathidicida. Although feral pigs can spread other plant pathogens, there is scant direct evidence that they act as vectors or transport hosts of P. agathidicida. Whether this is due to the lack of in-depth investigations, limitations in current detection methods, or simply that feral pigs are not playing a substantial role in the spread of kauri dieback disease is currently unknown. If management agencies proceed with a management strategy for feral pigs such as sustained control or eradication, under the assumption that this will mitigate unwanted impacts on kauri, an adaptive management approach should be taken to increase our understanding of the importance of feral pigs in this system. [ABSTRACT FROM AUTHOR]