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Fungal communities inhabiting plant tissues are complex systems of inter-species interactions, consisting of both the "abundant biosphere" and "rare biosphere". However, the composition, assembly, and stability of these subcommunities, as well as their contributions to productivity remain unclear. In this study, the taxonomic and functional composition, co-occurrence, and ecological assembly of abundant and rare fungal subcommunities in different tissues of three Panax species were investigated. Abundant subcommunities were dominated by potential plant pathogens belonging to Microbotryomycetes, while saprotrophic fungi like Agaricomycetes and Mortierellomycetes were more prevalent in rare subcommunities. The rare taxa played a central role in upholding the stability of the fungal networks as driven by Dothideomycetes and Sordariomycetes. Homogeneous selection played a larger role in the assembly of abundant fungal subcommunities compared to the rare counterparts, which was more dominated by stochastically ecological drift in all plant species. Rare biospheres played a larger role in the accumulation of saponin compared to their abundant counterparts, especially in the leaf endosphere, which was mainly affected by environmental factors (Mg, pH, OC, and etc.). Furthermore, we found that rare species belonging to unidentified saprotrophs were associated with saponin formation. This study provides hypotheses for future experiments to understand mechanisms accounting for the variations in the composition and function of rare fungal subcommunities across different Panax species. [ABSTRACT FROM AUTHOR]

Pathogenic fungi employ numerous strategies to colonize plants, infect them, reduce crop yield and quality, and cause significant losses in agricultural production. The increasing use of chemical pesticides has led to various ecological and environmental issues, including the emergence of resistant weeds, soil compaction, and water pollution, all negatively impacting agricultural sustainability. Additionally, the extensive development of synthetic fungicides has adverse effects on animal and human health, prompting the exploration of alternative approaches and green strategies for phytopathogen control. Microorganisms living in sponges represent a promising source of novel bioactive secondary metabolites, potentially useful in developing new nematicidal and antimicrobial agents. This study focuses on extracting bioactive compounds from endosymbiotic bacteria associated with the marine sponge Hyrtios erect sp. (collected from NIOF Station, Hurghada, Red Sea, Egypt) using various organic solvents. Bacillus sp. was isolated and identified through 16 S rRNA gene sequencing. The biocidal activity of Bacillus gotheilii MSB1 extracts was screened against plant pathogenic bacteria, fungi, and nematodes. The n-butanol extract showed significant potential as a biological fungicide against Alternaria alternata and Fusarium oxysporum. Both n-hexane and ethyl acetate extracts exhibited negative impacts against the plant pathogenic bacteria Erwinia carotovora and Ralstonia solanacearum, whereas the n-butanol extract had a positive effect. Regarding nematicidal activity, ethyl acetate and n-butanol extracts demonstrated in-vitro activity against the root-knot nematode Meloidogyne incognita, which causes serious vegetable crop diseases, but the n-hexane extract showed no positive effects. The findings suggest that bioactive compounds from endosymbiotic bacteria associated with marine sponges, particularly B. gotheilii MSB1, hold significant potential as alternative biological control agents against plant pathogens. The n-butanol extract, in particular, displayed promising biocidal activities against various plant pathogenic fungi, bacteria, and nematodes. These results support further exploration and development of such bioactive compounds as sustainable, environmentally friendly alternatives to synthetic pesticides and fungicides in agricultural practices. [ABSTRACT FROM AUTHOR]

Local adaptation has been a central theme of eco-evolutionary research for decades. It is generally assumed that plant pathogens are locally adapted due to their standing interactions with biotic and abiotic factors in the ecosystem. Effectors, secreted small proteins encoded by pathogens, play critical roles in host–pathogen interactions, by activating host genotype-specific resistance, suppressing plant immunity, and playing other functions. In this study, we investigated the potential involvement of RXLR effector genes in ecological adaptation by examining the simple sequence repeat (SSR), virulence, and effector profiles in Phytophthora infestans isolates collected from two geographic regions differing in ecological environments. Genotypic analyses with SSR markers and virulence assays showed that the pathogen from the two regions shared genetic background but differed in virulence spectrums. High-throughput sequencing and expression analysis of 24 selected P. infestans isolates further showed variations in the RXLR effector repertoire, ranging from 536 to 548 for each isolate and the expression of effector genes was highly associated with the accumulation of homologous sRNA. Regional specific alleles were detected at 94 RXLR effector genes, and a specific accumulation of homologous 25–26 nt sRNAs was found at 67 RXLR effector genes. Two of the regional specific RXLR effector genes were confirmed to be virulence factors. Taken together, these results suggest that genomic and epigenetic variations in RXLR effector genes contribute significantly to the ecological adaptation of P. infestans populations and that regional specific effector genes will help to understand the adaptive landscape of pathogens and efficient use of host resistance genes. [ABSTRACT FROM AUTHOR]

Plant pathogens secrete nuclear effectors into the host nuclei to modulate the host immune system. Although several nuclear effectors of fungal pathogens have been recently reported, the molecular mechanism of NLS-associated transport vehicles of nuclear effectors and the roles of NLS in transcriptional reprogramming of host immunity genes remain enigmatic. We previously reported the MoHTR1, a nuclear effector of the rice blast fungus, Magnaporthe oryzae. MoHTR1 is translocated to rice nuclei but not in fungal nuclei. Here, we identify the core NLS (RxKK) responsible for MoHTR1's nuclear localization. MoHTR1 is translocated in the host nucleus through interaction with rice importin α. MoHTR1 NLS empowers it to translocate the cytoplasmic effectors of M. oryzae into rice nuclei. Furthermore, other nuclear effector candidates of the blast pathogen and rice proteins which have RxKK also exhibit nuclear localization, highlighting the crucial role of RxKK in this process. We also unveil the importance of SUMOylation in the stability of MoHTR1 and translocation of MoHTR1 to host nuclei. Moreover, MoHTR1 NLS is essential for the pathogenicity of M. oryzae by reprogramming immunity-associated genes in the host. Our findings provide insights into the significance of plant-specific NLS on fungal nuclear effectors and its role in plant-pathogen interactions. Nuclear effectors of plant pathogens modulate the host immunity. Here, Lim et al. unveiled the core sequence and mechanism for nuclear localization of the rice blast fungal effector, MoHTR1, revealing its role in regulating the host immune system. [ABSTRACT FROM AUTHOR]

Introduction: Understanding the microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense is crucial for unraveling the plant–microbe interactions that influence its medicinal properties. Methods: This study is the first to characterize the microbiome associated with the rhizocompartments of D. huoshanense , including its cultivation medium, rhizosphere, rhizoplane, and root endosphere, using high-throughput sequencing and subsequent bioinformatic analysis. Results: Bacterial phylogenetic diversity was significantly higher in the endosphere than in the rhizosphere, while fungal α-diversity significantly decreased from the cultivation medium to the endosphere. Both bacterial and fungal niche widths decreased from the cultivation medium to the endosphere. β-Diversity analysis revealed distinct spatial patterns in both bacterial and fungal communities across the rhizocompartments, with the most pronounced differences between the cultivation medium and the endosphere. Taxonomically, Proteobacteria and Ascomycota were predominant in the endosphere for bacterial and fungal communities, respectively. Functional predictions showed significant enrichment of pathways related to xenobiotics biodegradation, lipid metabolism, and nitrogen fixation in the endosphere, while functions associated with plant pathogens and saprotrophs were significantly reduced. Discussion: The results indicate a shift from generalist to specialist microbes from the cultivation medium to the endosphere, suggesting that D. huoshanense exerts strong selective pressure for endophytic fungi. Interestingly, a high proportion of fungi with unknown functions were found in the endosphere, highlighting an area for further research regarding the medicinal efficacy of D. huoshanense. Overall, this study provides foundational data for understanding the adaptive evolution of these microbial communities in response to specific microhabitats. [ABSTRACT FROM AUTHOR]

Epigenetics has emerged as a potent field of study for understanding the factors influencing the effectiveness of human disease treatments and for identifying alternations induced by pathogens in host plants. However, there has been a paucity of research on the epigenetic control of the proliferation and pathogenicity of fungal plant pathogens. Fungal plant pathogens such as Magnaporthe oryzae , a significant threat to global rice production, provide an important model for exploring how epigenetic mechanisms govern fungal proliferation and virulence. In M. oryzae , epigenetic alterations, such as DNA methylation, histone modification, and non-coding RNAs, regulate gene expression patterns that influence the pathogen's ability to infect its host. These modifications can enhance fungal adaptability, allowing the pathogen to survive in diverse environments and evade host immune responses. Our primary objective is to provide a comprehensive review of the existing epigenetic research on M. oryzae and shed light on how these changes influence the pathogen's lifecycle, its ability to invade host tissues, and the overall severity of the disease. We begin by examining the epigenetic alterations occurring in M. oryzae and their contributions to the virulence and proliferation of the fungus. To advance our understanding of epigenetic mechanisms in M. oryzae and similar plant diseases, we emphasize the need to address unanswered questions and explore future research directions. This information is crucial for developing new antifungal treatments that target epigenetic pathways, which could lead to improved disease management. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Summary Wine production has a significant impact on the global economy. Despite this, the microbial composition of the terroir has not been studied sufficiently, particularly in the southern hemisphere. Here, we investigated how bulk soil fungal communities are affected by several abiotic and biotic factors across 1,000 km of Chilean vineyards. We found that geographical distance was the main driver of vineyard soil fungal communities. Irrespective of variety, older vineyards host a higher relative abundance of arbuscular mycorrhizal fungi (AMF) and a lower relative abundance of plant pathogenic fungi. This result could lead to significant recommendations on when to apply AMF‐based inoculants. The microbial dimension of the terroir has been increasingly recognized as an essential factor determining vineyard productivity and quality. Despite this, few studies have analyzed the factors affecting soil fungal communities of vineyards in the southern hemisphere. Across a 1,000 km gradient encompassing 34 Chilean vineyards, we investigated the effects of grapevine variety, geographical distance, maturity, and soil chemical properties on the diversity and composition of soil fungi. We implemented standard soil chemical analyses and ITS‐based DNA metabarcoding of bulk soil. We found that the total soil fungal composition was significantly affected by geographical distance but not by grapevine variety and maturity. Soil chemical dissimilarity also significantly affected soil fungal composition. When analyzing specific fungal guilds, we found a contrasting successional pattern: arbuscular mycorrhizal fungal relative abundance was significantly higher at medium and old‐maturity vineyards compared with young vineyards, on which plant pathogenic fungi had a markedly lower abundance. Our results present several caveats: the molecular marker was not the most commonly used for arbuscular mycorrhizal fungi, bulk soil was sampled (instead of roots), and all abundances were relative. Still, this study constitutes one of the most extensive studies on soil fungi – both for vineyards and Chile – and might have practical implications, as knowing the drivers of fungal and mycorrhizal biodiversity can inform agricultural management decisions. [ABSTRACT FROM AUTHOR]

Plant pathogenic fungi provoke devastating agricultural losses and are difficult to control. How these organisms acquire micronutrients during growth in the host environment remains poorly understood. Here we show that efficient regulation of copper acquisition mechanisms is crucial for plant colonization and virulence in the soilborne ascomycete Fusarium oxysporum, the causal agent of vascular wilt disease in more than 150 different crops. Using a combination of RNA-seq and ChIP-seq, we establish a direct role of the transcriptional regulator Mac1 in activation of copper deficiency response genes, many of which are induced during plant infection. Loss of Mac1 impaired growth of F. oxysporum under low copper conditions and abolishes pathogenicity on tomato plants and on the invertebrate animal host Galleria mellonella. Importantly, overexpression of two Mac1 target genes encoding a copper reductase and a copper transporter was sufficient to restore virulence in the mac1 mutant background. Our results establish a previously unrecognized role of copper reduction and uptake in fungal infection of plants and reveal new ways to protect crops from phytopathogens. Author summary: Fusarium oxysporum is the causal agent of vascular wilt disease and an opportunistic pathogen of humans. How fungal pathogens obtain micronutrients, such as metal ions, during growth inside the host remains unclear. The role of copper acquisition during fungal infection has been investigated in human pathogenic fungi but so far never in a plant pathogen. Here, we show that efficient regulation of copper uptake mechanisms, including copper reduction in the extracellular space and its internalization into the cytoplasm, is critical for effective plant colonization and virulence in F. oxysporum. Genes encoding metalloreductases and high-affinity copper transporters, whose activation is directly mediated by the copper-responsive transcription factor Mac1 and is required for growth under copper-limiting conditions, are transcriptionally induced during colonization of plant roots. Inactivation of Mac1 reduces growth of F. oxysporum during copper limitation and abolishes pathogenicity on tomato plants. Importantly, we provide evidence that the loss-of-virulence phenotype of the mac1 null mutant is strictly linked with its inability to acquire copper. Since copper is found primarily in its oxidized form in the xylem vessels of tomato plants, our work suggests that targeting copper acquisition mechanisms may represent a promising strategy for controlling diseases caused by phytopathogenic fungi. [ABSTRACT FROM AUTHOR]

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]

Introduction: Pantoea ananatis has emerged as a significant plant pathogen affecting various crops worldwide, causing substantial economic losses. Bacteriophages and their endolysins offer promising alternatives for controlling bacterial infections, addressing the growing concerns of antibiotic resistance. Methods: This study isolated and characterized the Pantoea phage PA1 and investigated the role of PA1-LRP in directly damaging bacteria and assisting endolysin PA1-Lys in cell lysis, comparing its effect to exogenous transmembrane domains following the identification and analysis of the PA1-Lys and the PA1-LRP based on whole genome analysis of phage PA1. Additionally, this study also explored how hydrophobic region of PA1-LRP (HPP) contributes to bacterial killing when combined with PA1-Lys and examined the stability and lytic spectrum of PA1-Lys under various conditions. Results and discussion: Phage PA1 belonging to the Chaseviridae family exhibited a broad host range against P. ananatis strains, with a latent period of 40 minutes and a burst size of 17.17 phages per infected cell. PA1-Lys remained stable at pH 6-10 and temperatures of 20-50°C and showed lytic activity against various Gram-negative bacteria, while PA1-Lys alone could not directly lyse bacteria, its lytic activity was enhanced in the presence of EDTA. Surprisingly, PA1-LRP inhibited bacterial growth when expressed alone. After 24 h of incubation, the OD600 value of pET28a-LRP decreased by 0.164 compared to pET28a. Furthermore, the lytic effect of co-expressed PA1-LRP and PA1-Lys was significantly stronger than each separately. After 24 h of incubation, compared to pET28a-LRP, the OD600 value of pET28a-Lys-LRP decreased by 0.444, while the OD420 value increased by 3.121. Live/dead cell staining, and flow cytometry experiments showed that the fusion expression of PA1-LRP and PA1-Lys resulted in 41.29% cell death, with bacterial morphology changing from rod-shaped to filamentous. Notably, PA1-LRP provided stronger support for endolysin-mediated cell lysis than exogenous transmembrane domains. Additionally, our results demonstrated that the HPP fused with PA1-Lys, led to 40.60% cell death, with bacteria changing from rod-shaped to spherical and exhibiting vacuolation. Taken together, this study provides insights into the lysis mechanisms of Pantoea phages and identifies a novel lysis-related protein, PA1-LRP, which could have potential applications in phage therapy and bacterial disease control. [ABSTRACT FROM AUTHOR]

Honeybee larvae and pupae form the cornerstone of colony survival, development, and reproduction. Azoxystrobin is an effective strobilurin fungicide that is applied during the flowering stage for controlling plant pathogens. The contaminated nectar and pollen resulting from its application are collected by forager bees and impact the health of honeybee larvae and pupae. The current study evaluated the survival, development, and physiological effects of azoxystrobin exposure on the larvae and pupae of Apis mellifera worker bees. The field-recommended concentrations of azoxystrobin were found to suppress the survival indices and lifespan in the larval as well as pupal stages; moreover, the rates of the survival and pupation of larvae as well as the body weights of the pupae and newly-emerged adult bees were significantly reduced upon long-term exposure to azoxystrobin. In addition, azoxystrobin ingestion induced changes in the expression of genes critical for the development, immunity, and nutrient metabolism of larvae and pupae, although the expression profile of these genes differed between the larval and pupal stages. Results indicated the chronic toxicity of azoxystrobin on the growth and development of honeybee larvae and pupae, which would affect their sensitivity to pathogens and other external stresses during the development stage and the study will provide vital information regarding the pollination safety and rational use of pesticides. [ABSTRACT FROM AUTHOR]

The editorial discusses the significant role of microorganisms and their metabolites in agriculture, food production, and environmental sustainability. Microbes like plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi enhance soil fertility and crop resilience, while microbial metabolites offer eco-friendly biocontrol solutions. Research highlights the potential of engineered microbial communities for sustainable agriculture, food safety, and environmental restoration, emphasizing the need for further exploration in optimizing microbial interactions and biodegradation pathways. The studies presented in the editorial showcase advancements in leveraging microorganisms for various applications, underscoring the importance of microbial solutions in achieving global food security and environmental health. [Extracted from the article]

Summary: Hosts and pathogens typically engage in a coevolutionary arms race. This also applies to phytopathogenic powdery mildew fungi, which can rapidly overcome plant resistance and perform host jumps.Using experimental evolution, we show that the powdery mildew pathogen Blumeria hordei is capable of breaking the agriculturally important broad‐spectrum resistance conditioned by barley loss‐of‐function mlo mutants.Partial mlo virulence of evolved B. hordei isolates is correlated with a distinctive pattern of adaptive mutations, including small‐sized (c. 8–40 kb) deletions, of which one is linked to the de novo insertion of a transposable element. Occurrence of the mutations is associated with a transcriptional induction of effector protein‐encoding genes that is absent in mlo‐avirulent isolates on mlo mutant plants. The detected mutational spectrum comprises the same loci in at least two independently isolated mlo‐virulent isolates, indicating convergent multigenic evolution. The mutational events emerged in part early (within the first five asexual generations) during experimental evolution, likely generating a founder population in which incipient mlo virulence was later stabilized by additional events.This work highlights the rapid dynamic genome evolution of an obligate biotrophic plant pathogen with a transposon‐enriched genome. [ABSTRACT FROM AUTHOR]

Hydroponic greenhouses and vertical farms provide an alternative crop production strategy in regions that experience low temperatures, suboptimal sunlight, or inadequate soil quality. However, hydroponic systems are soilless and, therefore, have vastly different bacterial microbiota than plants grown in soil. This review highlights some of the most prevalent plant growth-promoting bacteria (PGPB) and destructive phytopathogenic bacteria that dominate hydroponic systems. A complete understanding of which bacteria increase hydroponic crop yields and ways to mitigate crop loss from disease are critical to advancing microbiome research. The section focussing on plant growth-promoting bacteria highlights putative biological pathways for growth promotion and evidence of increased crop productivity in hydroponic systems by these organisms. Seven genera are examined in detail, including Pseudomonas, Bacillus, Azospirillum, Azotobacter, Rhizobium, Paenibacillus, and Paraburkholderia. In contrast, the review of hydroponic phytopathogens explores the mechanisms of disease, studies of disease incidence in greenhouse crops, and disease control strategies. Economically relevant diseases caused by Xanthomonas, Erwinia, Agrobacterium, Ralstonia, Clavibacter, Pectobacterium, and Pseudomonas are discussed. The conditions that make Pseudomonas both a friend and a foe, depending on the species, environment, and gene expression, provide insights into the complexity of plant–bacterial interactions. By amalgamating information on both beneficial and pathogenic bacteria in hydroponics, researchers and greenhouse growers can be better informed on how bacteria impact modern crop production systems. [ABSTRACT FROM AUTHOR]

Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, poses a significant threat to sugarcane cultivation. An obligate parasite, phytoplasma is difficult to culture in laboratory conditions, making the isolation of its DNA from the massive amount of plant host DNA extremely challenging. Yet, the appropriate amount and quality of plant microbiome-derived DNA are key for high-quality DNA sequencing data. Here, a simple, cost-effective, alternative method for DNA isolation was applied using a guanidine-HCl-hydroxylated silica (GuHCl-Silica)-based method and microbiome DNA enrichment based on size-selective low-molecular-weight (LMW) DNA by PEG/NaCl precipitation. qPCR analysis revealed a significant enrichment of phytoplasma DNA in the LMW fraction. Additionally, the NEBNext Microbiome DNA enrichment kit was utilized to further enrich microbial DNA, demonstrating a remarkable increase in the relative abundance of phytoplasma DNA to host DNA. Shotgun sequencing of the isolated DNA gave high-quality data on the metagenome assembly genome (MAG) of Ca. Phytoplasma sacchari SCWL with completeness at 95.85 and 215× coverage. The results indicate that this combined approach of PEG/NaCl size selection and microbiome enrichment is effective for obtaining high-quality genomic data from phytoplasma, surpassing previous methods in efficiency and resource utilization. This low-cost method not only enhances the recovery of microbiome DNA from plant hosts but also provides a robust framework for studying plant pathogens in complex plant models. [ABSTRACT FROM AUTHOR]

Fungicides are used to control phytopathogens but all these fungicides have deleterious effects. Allelopathic interactions can be harnessed as a natural way to control the pathogens but there are no reports that show the allelopathic interactions of donor plant, recipient crop, as well as the target plant pathogen and the material used for inoculum production. So, in the present study, the suitability of Carthamus oxyacantha M. Bieb. was assessed against Macrophomina phaseolina, the cause of charcoal rot in maize. Among the various treatments in pot experiment, a negative control, 3 concentrations of inoculum (1.2×105, 2.4×105, and 3.6×105 colony forming units (CFU) mL-1, 3 concentrations (0.5, 1.0, and 1.5% w/w) of C. oxyacantha along with an autoclaved M. phaseolina (Mp) and C. oxyacantha alone were included to investigate their allelopathic effects on maize, not investigated earlier. Maximum suppression of the disease was observed by 1.5% (w/w) concentration of C. oxyacantha. Soil amendment with C. oxyacantha significantly suppressed the disease incidence (DI) and disease severity index (DSI) in charcoal rot of maize up to 40 and 55%, respectively over the strongest level of inoculum (Mp3). C. oxyacantha not only reduced area under disease incidence progress curve (AUDIPC) and area under disease severity progress curve (AUDSPC), but also improved the morphological, biochemical and physiological parameters of maize. The maximum increase of 48, 65, and 75% in values of shoot length (SL), shoot dry mass (SDM), and root dry mass (RDM), respectively was observed by application of the highest concentration of C. oxyacantha in the treatment Mp1+Co3, over infested control (Mp1). Photosynthetic pigments, such as chlorophyll a, chlorophyll b and carotenoids were increased to 58, 64, and 46%, respectively over Mp1, by the application of C. oxyacantha. Carbon assimilation rate (A), stomatal conductance (gs), rate of transpiration (E), and internal carbon dioxide concentration (Ci) were significantly increased to 58, 48, 48, and 20%, respectively over infested control (Mp3), by application of C. oxyacantha concentration 1.5 (w/w). Moreover, defense enzymes like superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities were boosted up to 27, 28, and 28% over Mp3, respectively. Positive allelopathy of C. oxyacantha towards maize and negative allelopathy towards M. phaseolina makes C. oxyacantha a suitable candidate for charcoal rot disease control in maize. [ABSTRACT FROM AUTHOR]

Biofilms are major virulence factors formed by pathogenic bacteria to invade their host and maintain their colony. While biofilms usually develop on diverse solid surfaces, floating biofilms, also called pellicles, are formed at the air–liquid interface. To address the problem of biofilm formation by bacterial pathogens, honey has been extensively studied. However, information on the effect of honey on biofilm formation by plant pathogens is scarce. This study aimed to determine the effects of manuka honey on biofilm and pellicle formation by Pectobacterium brasiliense and analyze the expression of genes encoding proteins needed to form biofilm by using semiquantitative PCR and RT‐qPCR. Treatment with 5% (w/v) of manuka honey significantly decreased biofilm and pellicle formation by P. brasiliense. RT‐qPCR results showed that the expression of bcsA, fis, hrpL, and expI decreased 7.07‐fold, 5.71‐fold, 13.11‐fold, and 6.26‐fold, respectively, after exposure to 5% (w/v) manuka honey. Our findings reveal that manuka honey may effectively inhibit biofilm and pellicle formation. [ABSTRACT FROM AUTHOR]

Pathogenic microorganisms often target seedlings shortly after germination. If plants exhibit resistance or resilience to pathogens, those exposed to pathogen challenge may grow further and form new unchallenged leaves. The purpose of this study was to examine disease resistance in the newly formed leaves of plants subjected to pathogen challenge. We used Arabidopsis thaliana and the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) as the model pathosystem. We found that Arabidopsis seedlings primarily challenged with the avirulent isolate Hpa exhibited enhanced disease resistance against the virulent isolate Hpa in newly formed rosette leaves (NFRLs). Our observations indicated that the transcript levels of the transcription factor gene WRKY70, which is essential for full resistance to the virulent isolate HpaNoco2, were elevated and maintained at high levels in the NFRLs. In contrast, the transcript levels of the salicylic acid marker gene PR1 and systemic acquired resistance‐related genes did not exhibit sustained elevation. The maintenance of increased transcript levels of WRKY70 operated independently of non‐expressor of pathogenesis‐related gene 1. These findings suggest that prolonged upregulation of WRKY70 represents a defensive state synchronized with plant development to ensure survival against subsequent infections. [ABSTRACT FROM AUTHOR]

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens. Author summary: Plant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies of Peronospora effusa. This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen. [ABSTRACT FROM AUTHOR]

ABSTRACT Root‐knot nematodes (RKNs; Meloidogyne spp.) are a serious threat to crop production. The competition between plants and pathogens for assimilates influences the outcome of their interactions. However, the mechanisms by which plants and nematodes compete with each other for assimilates have not been elucidated. In this study, we demonstrated that miR396a plays a negative role in defense against RKNs and a positive role in sugar accumulation in tomato roots. The overexpression of SlGRF8 (Solanum lycopersicum growth‐regulating factor 8), the target of miR396a, decreased the sugar content of the roots and the susceptibility to RKNs, whereas the grf8‐cr mutation had the opposite effects. Furthermore, we confirmed that SlGRF8 regulated the sugar content in roots by directly activating the transcription of SlSTP10 (Solanum lycopersicum sugar transporter protein 10) in response to RKN stress. Moreover, SlSTP10 was expressed primarily in the tissues surrounding giant cells, and the SlSTP10 knockout increased both the sugar content in the roots and the plant's susceptibility to RKNs. Overall, this study provides important insight into the molecular mechanism through which the miR396a‐SlGRF8‐SlSTP10 module regulates sugar allocation in roots under RKN stress. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the effects of Bacillus velezensis Bv-116 and its bio-organic fertilizer on the control of cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. Cucumerinum (FOC), the promotion of growth of cucumber seedlings, and the soil microbial community. B. velezensis Bv-116 exhibited an inhibition rate of 84.93% against FOC, as well as broad-spectrum inhibitory activities against other soil-borne plant pathogenic fungi. Fermentation products of B. velezensis Bv-116 destroyed the cell structure of FOC and inhibited the growth of FOC mycelium. These products were identified as volatile antimicrobial gases, proteases and cellulases. In the greenhouse pot experiment, both B. velezensis Bv-116 and its bio-organic fertilizer exhibited significant promoting effects on cucumber growth, and a significant reduction in the incidence and disease severity index of cucumber wilt (p < 0.05). Analysis of the microbial community structure of cucumber rhizosphere soil revealed that inoculation of B. velezensis Bv-116 and its bio-organic fertilizer increased the abundance of genera with biocontrol capabilities against plant pathogens. In addition, inoculation of the bio-organic fertilizer reversed the excessive proliferation of Fusarium and Acidobacteria. Our results suggest the potential of inoculating B. velezensis Bv-116 and its bio-organic fertilizer as an environmentally friendly biocontrol strategy against cucumber wilt. [ABSTRACT FROM AUTHOR]

Background: Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown. Results: Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum. Conclusions: Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. 6HVRaGfzCN9g8_uHWKg5j1 Video Abstract [ABSTRACT FROM AUTHOR]

Elsinoë species are phytopathogenic fungi that cause serious scab diseases on economically important plants. The disease symptoms arise from the effects of a group of phytotoxins known as elsinochromes, produced via a type-I polyketide synthase (PKS) biosynthetic pathway. The elsinochrome gene cluster was first annotated in Elsinoë fawcettii where the main type-I PKS gene was characterized as EfPKS1. A later study showed that this gene and the associated cluster had not been correctly annotated, and that EfPKS1 was actually the anchor gene of the melanin biosynthetic pathway. A new type-I PKS gene EfETB1 associated with elsinochrome production was also identified. The aim of this study was to identify all type-I PKS genes in the genomes of seven Elsinoë species with the goal of independently verifying the PKS containing clusters for both melanin and elsinochrome production. A total of six type-I PKS classes were identified, although there was variation between the species in the number and type of classes present. Genes similar to the E. fawcettii EfPKS1 and EfETB1 type-I PKS genes were associated with melanin and elsinochrome production respectively in all species. The complete melanin and elsinochrome PKS containing clusters were subsequently annotated in all the species with high levels of synteny across Elsinoë species. This study provides a genus-level overview of type-I PKS distribution in Elsinoë species, including an additional line of support for the annotation of the melanin and elsinochrome PKS containing clusters in these important plant pathogens. [ABSTRACT FROM AUTHOR]

Peptidoglycan (PG), a mesh-like structure which is the primary component of the bacterial cell wall, is crucial to maintain cell integrity and shape. While most bacteria rely on penicillin binding proteins (PBPs) for crosslinking, some species also employ LD-transpeptidases (LDTs). Unlike PBPs, the essentiality and biological functions of LDTs remain largely unclear. The Hyphomicrobiales order of the Alphaproteobacteria, known for their polar growth, have PG which is unusually rich in LD-crosslinks, suggesting that LDTs may play a more significant role in PG synthesis in these bacteria. Here, we investigated LDTs in the plant pathogen Agrobacterium tumefaciens and found that LD-transpeptidation, resulting from at least one of 14 putative LDTs present in this bacterium, is essential for its survival. Notably, a mutant lacking a distinctive group of 7 LDTs which are broadly conserved among the Hyphomicrobiales exhibited reduced LD-crosslinking and tethering of PG to outer membrane β-barrel proteins. Consequently, this mutant suffered severe fitness loss and cell shape rounding, underscoring the critical role played by these Hyphomicrobiales-specific LDTs in maintaining cell wall integrity and promoting elongation. Tn-sequencing screens further revealed non-redundant functions for A. tumefaciens LDTs. Specifically, Hyphomicrobiales-specific LDTs exhibited synthetic genetic interactions with division and cell cycle proteins, and a single LDT from another group. Additionally, our findings demonstrate that strains lacking all LDTs except one displayed distinctive phenotypic profiles and genetic interactions. Collectively, our work emphasizes the critical role of LD-crosslinking in A. tumefaciens cell wall integrity and growth and provides insights into the functional specialization of these crosslinking activities. Author summary: Peptidoglycan (PG) is essential for bacterial cell wall integrity. While most bacteria use penicillin binding proteins (PBPs) for crosslinking, some also employ LD-transpeptidases (LDTs); however, the essentiality and functions of LDTs remain poorly understood. Interestingly, Hyphomicrobiales bacteria have PG rich in LD-crosslinks, suggesting that LDTs play a vital role in maintaining cell wall integrity in these organisms. Our study of Agrobacterium tumefaciens revealed that LD-transpeptidation, mediated by at least one of 14 putative LDTs, is essential for maintaining both viability and morphogenesis. A mutant lacking 7 Hyphomicrobiales-specific LDTs suffered fitness and shape loss due to reduced LD-crosslinking and PG tethering to the outer membrane. Our results provide new insights into LD-transpeptidase specialized functions and conditional essentiality. The conservation of these enzymes across diverse polar-growing species suggests broader implications for understanding microbial cell wall growth and adaptation to environmental stresses. [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]

Polyamines (PAs), which are aliphatic polycationic compounds with a low molecular weight, are found in all living organisms and play essential roles in plant–pathogen interactions. Putrescine, spermidine, and spermine, the most common PAs in nature, respond to and function differently in plants and pathogens during their interactions. While plants use certain PAs to enhance their immunity, pathogens exploit PAs to facilitate successful invasion. In this review, we compile recent studies on the roles of PAs in plant–pathogen interactions, providing a comprehensive overview of their roles in both plant defense and pathogen pathogenicity. A thorough understanding of the functions of PAs and conjugated PAs highlights their potential applications in fungicide development. The creation of new fungicides and compounds derived from PAs demonstrates their promising potential for further research and innovation in this field. [ABSTRACT FROM AUTHOR]

Trichoderma spp. is known for its ability to enhance plant growth and suppress disease, but the mechanisms for its interaction with host plants and pathogens remain unclear. This study investigated the transcriptomics and metabolomics of peanut plants (Arachis hypogaea L.) inoculated with Trichoderma harzianum QT20045, in the absence and presence of the stem rot pathogen Sclerotium rolfsii JN3011. Under the condition without pathogen stress, the peanut seedlings inoculated with QT20045 showed improved root length and plant weight, increased indole acetic acid (IAA) production, and reduced ethylene level, with more active 1-aminocyclopropane-1-carboxylate acid (ACC) synthase (ACS) and ACC oxidase (ACO), compared with the non-inoculated control. Under the pathogen stress, the biocontrol efficacy of QT20045 against S. rolfsii was 78.51%, with a similar effect on plant growth, and IAA and ethylene metabolisms to the condition with no biotic stress. Transcriptomic analysis of peanut root revealed that Trichoderma inoculation upregulated the expression of certain genes in the IAA family but downregulated the genes in the ACO family (AhACO1 and AhACO) and ACS family (AhACS3 and AhACS1) consistently in the absence and presence of pathogens. During pathogen stress, QT20045 inoculation leads to the downregulation of the genes in the pectinesterase family to keep the host plant's cell wall stable, along with upregulation of the AhSUMM2 gene to activate plant defense responses. In vitro antagonistic test confirmed that QT20045 suppressed S. rolfsii growth through mechanisms of mycelial entanglement, papillary protrusions, and decomposition. Our findings highlight that Trichoderma inoculation is a promising tool for sustainable agriculture, offering multiple benefits from pathogen control to enhanced plant growth and soil health. [ABSTRACT FROM AUTHOR]

The fungal pathogen Didymella segeticola causes leaf spot and leaf blight on tea plant (Camellia sinensis), leading to production losses and affecting tea quality and flavor. Accurate detection and quantification of D. segeticola growth in tea plant leaves are crucial for diagnosing disease severity or evaluating host resistance. In this study, we monitored disease progression and D. segeticola development in tea plant leaves inoculated with a GFP-expressing strain. By contrast, a DNA-based qRT-PCR analysis was employed for a more convenient and maneuverable detection of D. segeticola growth in tea leaves. This method was based on the comparison of D. segeticola-specific DNA encoding a Cys2His2-zinc-finger protein (NCBI accession number: OR987684) in relation to tea plant Cs18S rDNA1. Unlike ITS and TUB2 sequences, this specific DNA was only amplified in D. segeticola isolates, not in other tea plant pathogens. This assay is also applicable for detecting D. segeticola during interactions with various tea cultivars. Among the five cultivars tested, 'Zhongcha102' (ZC102) and 'Fuding-dabaicha' (FDDB) were more susceptible to D. segeticola compared with 'Longjing43' (LJ43), 'Zhongcha108' (ZC108), and 'Zhongcha302' (ZC302). Different D. segeticola isolates also exhibited varying levels of aggressiveness towards LJ43. In conclusion, the DNA-based qRT-PCR analysis is highly sensitive, convenient, and effective method for quantifying D. segeticola growth in tea plant. This technique can be used to diagnose the severity of tea leaf spot and blight or to evaluate tea plant resistance to this pathogen. [ABSTRACT FROM AUTHOR]

Loop-Mediated Isothermal Amplification (LAMP) represents a valuable technique for DNA/RNA detection, known for its exceptional sensitivity, specificity, speed, accuracy, and affordability. This study focused on optimizing a LAMP-based method to detect early signs of Plasmopara halstedii, the casual pathogen of sunflower downy mildew, a severe threat to sunflower crops. Specifically, a set of six LAMP primers (two outer, two inner, and two loop) were designed from P. halstedii genomic DNA, targeting the ribosomal Large Subunit (LSU). These primers were verified by in silico analysis and experimental validation using both target and non-target species' DNAs. Optimizations encompassing reaction conditions (temperature, time) and component concentrations (magnesium, Bst DNA polymerase, primers, and dNTP) were determined. Validation of these optimizations was performed by agarose gel electrophoresis. Furthermore, various colorimetric chemicals (Neutral Red, Hydroxynaphthol Blue, SYBR Safe, Thiazole Green) were evaluated to facilitate method analysis, and the real-time analysis has been optimized, presenting multiple approaches for detecting sunflower downy mildew using the LAMP technique. The analytical sensitivity of the method was confirmed by detecting P. halstedii DNA concentrations as low as 0.5 pg/μl. This pioneering study, establishing P. halstedii detection through the LAMP method, stands as unique in its field. The precision, robustness, and practicality of the LAMP protocol make it an ideal choice for studies focusing on sunflower mildew, emphasizing its recommended use due to its operational ease and reliability. [ABSTRACT FROM AUTHOR]

Introduction: Understanding the microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense is crucial for unraveling the plant--microbe interactions that influence its medicinal properties. Methods: This study is the first to characterize the microbiome associated with the rhizocompartments of D. huoshanense, including its cultivation medium, rhizosphere, rhizoplane, and root endosphere, using high-throughput sequencing and subsequent bioinformatic analysis. Results: Bacterial phylogenetic diversity was significantly higher in the endosphere than in the rhizosphere, while fungal α-diversity significantly decreased from the cultivation medium to the endosphere. Both bacterial and fungal niche widths decreased from the cultivation medium to the endosphere. β-Diversity analysis revealed distinct spatial patterns in both bacterial and fungal communities across the rhizocompartments, with the most pronounced differences between the cultivation medium and the endosphere. Taxonomically, Proteobacteria and Ascomycota were predominant in the endosphere for bacterial and fungal communities, respectively. Functional predictions showed significant enrichment of pathways related to xenobiotics biodegradation, lipid metabolism, and nitrogen fixation in the endosphere, while functions associated with plant pathogens and saprotrophs were significantly reduced. Discussion: The results indicate a shift from generalist to specialist microbes from the cultivation medium to the endosphere, suggesting that D. huoshanense exerts strong selective pressure for endophytic fungi. Interestingly, a high proportion of fungi with unknown functions were found in the endosphere, highlighting an area for further research regarding the medicinal efficacy of D. huoshanense. Overall, this study provides foundational data for understanding the adaptive evolution of these microbial communities in response to specific microhabitats. [ABSTRACT FROM AUTHOR]

The control of fungal and bacterial plant diseases mainly relies on the application of mineral and chemical fungicides/bactericides, which are considered to be environmental pollutants and toxic to humans. Moreover, the prolonged use of bactericides and antibiotics has led to the development of resistance among pathogens, as well as an increase in environmental and health threats. Therefore, the development of non-toxic and non-polluting treatments to control plant diseases has been the focus of extensive research in agriculture. Synthetic antimicrobial peptides have recently received extensive attention as the potential alternatives to other conventional methods in terms of their strong broad-spectrum antimicrobial activity. In vitro assays using various chemically synthesized peptides showed that the broad-spectrum peptide thanatin derived from the spined soldier bug (Podisus maculiventris (Say)) had the greatest potential for eliminating aflatoxigenic fungi. However, the antibacterial effect of thanatin against bacterial plant pathogens was less studied so far. The thanatin encoding sequence was codon optimized for expression in Pichia pastoris. This coding sequence cloned into P. pastoris expression vector pPICZαA and used for synthetizing the recombinant thanatin. Then, antibacterial activities of the constructed peptide were studied under in vitro and in vivo condition. The result showed that, all construction, cloning and expression processes were successfully performed in yeast. The results of the MIC and MBC tests showed that the growth rate of the majority of bacterial plant pathogens including gram-negative and gram-positive bacteria was inhibited by recombinant thanatin under in vitro conditions. MIC values for different bacterial isolates ranged from 0.016 to 2.048, while the MBC values for the same bacterial isolates were determined to be between 0.064 and 4.096 μg/mL. These amounts were significantly lower than the MIC and MBC values obtained by applying copper oxychloride. The application of 4.09 μg/mL of recombinant thanatin against rice leaf blight splendidly controlled this bacterial disease under greenhouse conditions. However, this promising antimicrobial peptide requires further investigation for the development of novel molecules for the control of plant pathogens. [ABSTRACT FROM AUTHOR]

Summary: In photosynthetic cells, plants convert carbon dioxide to sugars that can be moved between cellular compartments by transporters before being subsequently metabolized to support plant growth and development. Most pathogens cannot synthesize sugars directly but have evolved mechanisms to obtain plant‐derived sugars as C resource for successful infection and colonization. The availability of sugars to pathogens can determine resistance or susceptibility. Here, we summarize current progress on the roles of sugar transporters in plant–pathogen interactions. We highlight how transporters are manipulated antagonistically by both host and pathogens in competing for sugars. We examine the potential application of this target in resistance breeding and discuss opportunities and challenges for the future. [ABSTRACT FROM AUTHOR]

Autophagy, an intracellular degradation process, has emerged as a crucial innate immune response against various plant pathogens, including viruses. Tomato spotted wilt orthotospovirus (TSWV) is a highly destructive plant pathogen that infects over 1000 plant species and poses a significant threat to global food security. However, the role of autophagy in defence against the TSWV pathogen, and whether the virus counteracts this defence, remains unknown. In this study, we report that autophagy plays an important role in antiviral defence against TSWV infection; however, this autophagy‐mediated defence is counteracted by the viral effector NSs. Transcriptome profiling revealed the up‐regulation of autophagy‐related genes (ATGs) upon TSWV infection. Blocking autophagy induction by chemical treatment or knockout/down of ATG5/ATG7 significantly enhanced TSWV accumulation. Notably, the TSWV nucleocapsid (N) protein, a major component of the viral replication unit, strongly induced autophagy. However, the TSWV nonstructural protein NSs was able to effectively suppress N‐induced autophagy in a dose‐dependent manner. Further investigation revealed that NSs inhibited ATG6‐mediated autophagy induction. These findings provide new insights into the defence role of autophagy against TSWV, a representative segmented negative‐strand RNA virus, as well as the tospoviral pathogen counterdefence mechanism. [ABSTRACT FROM AUTHOR]

Cotton (Gossypium spp.) is the most important fibre crop worldwide. Black root rot and Fusarium wilt are two major diseases of cotton caused by soil-borne Berkeleyomyces rouxiae and Fusarium oxysporum f. sp. vasinfectum (Fov), respectively. Phenotyping plant symptoms caused by soil-borne pathogens has always been a challenge. To increase the uniformity of infection, we adapted a seedling screening method that directly uses liquid cultures to inoculate the plant roots and the soil. Four isolates, each of B. rouxiae and Fov, were collected from cotton fields in Australia and were characterised for virulence on cotton under controlled plant growth conditions. While the identities of all four B. rouxiae isolates were confirmed by multilocus sequencing, only two of them were found to be pathogenic on cotton, suggesting variability in the ability of isolates of this species to cause disease. The four Fov isolates were phylogenetically clustered together with the other Australian Fov isolates and displayed both external and internal symptoms characteristic of Fusarium wilt on cotton plants. Furthermore, the isolates appeared to induce varied levels of plant disease severity indicating differences in their virulence on cotton. To contrast the virulence of the Fov isolates, four putatively non-pathogenic Fusarium oxysporum (Fo) isolates collected from cotton seedlings exhibiting atypical wilt symptoms were assessed for their ability to colonise cotton host. Despite the absence of Secreted in Xylem genes (SIX6, SIX11, SIX13 and SIX14) characteristic of Fov, all four Fo isolates retained the ability to colonise cotton and induce wilt symptoms. This suggests that slightly virulent strains of Fo may contribute to the overall occurrence of Fusarium wilt in cotton fields. Findings from this study will allow better distinction to be made between plant pathogens and endophytes and allow fungal effectors underpinning pathogenicity to be explored. [ABSTRACT FROM AUTHOR]

Trichoderma species have been reported as masters in producing cellulolytic enzymes for the biodegradation of lignocellulolytic biomass and biocontrol agents against plant pathogens and pests. In our previous study, a novel Trichoderma strain LZ117, which shows potent capability in cellulase production, was isolated. Herein, we conducted multilocus phylogenetic analyses based on DNA barcodes and performed time-scaled phylogenomic analyses using the whole genome sequences of the strain, annotated by integrating transcriptome data. Our results suggest that this strain represents a new species closely related to T. atrobrunneum (Harzianum clade). Genes encoding carbohydrate-active enzymes (CAZymes), transporters, and secondary metabolites were annotated and predicted secretome in Trichoderma sp. LZ117 was also presented. Furthermore, genetic manipulation of this strain was successfully achieved using PEG-mediated protoplast transformation. A putative transporter gene encoding maltose permease (Mal1) was overexpressed, which proved that this transporter does not affect cellulase production. Moreover, overexpressing the native Cre1 homolog in LZ117 demonstrated a more pronounced impact of glucose-caused carbon catabolite repression (CCR), suggesting the importance of Cre1-mediated CCR in cellulase production of Trichoderma sp. LZ117. The results of this study will benefit further exploration of the strain LZ117 and related species for their applications in bioproduction. [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]

Some basic aspects of plant disease epidemiology remain largely unknown due to a lack of empirical study methods to experimentally manipulate the position of infections within a single plant or within a plant canopy and the dispersal behaviors of small insects that vector important plant diseases, for example. We present two methods using UV fluorescent particles that, when mixed in a 10% ethanol solution, can be used to create surrogate fungal infections on plant leaves and to field mark whiteflies in situ. When we used a custom-made experimental chamber to measure the velocity of falling particles, we found that the UV fluorescent particles had settlement velocities that overlapped with known fungal plant pathogen spores. In a separate experiment, field applied marks to whiteflies, Bemisia tabaci, were used to estimate straight-line insect vector displacement from source plants as a simple dispersal gradient over a limited distance in a 48 h period. The UV fluorescent particles and airbrushes were relatively inexpensive (USD < 100 total), easily sourced, and usable in a field setting. We believe that the approaches and methods shared in this manuscript can be used to design specific experiments that will fill important plant epidemiological knowledge gaps in future studies. [ABSTRACT FROM AUTHOR]

Ensuring global food security amid mounting challenges, such as population growth, disease infestations, resource limitations, and climate change, is a pressing concern. Anticipated increases in food demand add further complexity to this critical issue. Plant pathogens, responsible for substantial crop losses (up to 41%) in major crops like wheat, rice, maize, soybean, and potato, exacerbate the situation. Timely disease detection is crucial, yet current practices often identify diseases at advanced stages, leading to severe infestations. To address this, remote sensing and Hyperspectral imaging (HSI) have emerged as robust and nondestructive techniques, exhibiting promising results in early disease identification. Integrating machine learning algorithms with image data sets enables precise spatial–temporal disease identification, facilitating timely detection, predictive modeling, and effective disease management without compromising fitness or climate adaptability. By harnessing these cutting-edge technologies and data-driven decision-making, growers can optimize input costs while achieving enhanced yields, making significant strides toward global food security in the face of climate change risks. This review will discuss some of the foundational concepts of remote sensing, several platforms used for remote sensing data collection, successful application of the approach, and its future perspective. [ABSTRACT FROM AUTHOR]

Tomato is an economically and nutritionally important crop and is vulnerable to drought. Under drought, soil microbes provide beneficial effects to plants and alleviate stress. We suggest a reconstruction of the soil microbiome using biofumigation, an organic farming method, to protect tomatoes. In this study, we treated soil in four ways with varied concentrations: biofumigation (BF0.5, BF1.0, and BF1.5), green manure treatment (GM0.5, GM1.0, and GM1.5), autoclaving (AT), and non-treatment (NT). Tomatoes were grown in each treated soil, subjected to water shortages, and were rewatered. We investigated plant phenotypes and soil properties, focused on microbial communities using the Illumina MiSeq® System. Relative Water Content and malondialdehyde were measured as plant stress. The results showed that the 1% biofumigation treatment had 105% and 108.8% RWC during drought and after rewatering, compared to the non-treated soil. The highest concentration, the 1.5% treatment, lowered RWC due to an excess of NO3−, K+, Ca2+, and decreased alpha diversity. Through PLS-PM, bacterial alpha diversity was found to be the largest factor in the increase in RWC (coefficient = 0.3397), and both biofumigant and green manure significantly increased the Shannon index and observed species. In addition, biofumigation increased beneficial functional genes (purine metabolism, pyrimidine metabolism, carbon fixation pathways, and zeatin bio-synthesis) of soil microorganisms (p value < 0.05, <0.01, >0.05, and <0.05, respectively). The 1% biofumigation treatment enriched the core five genera of the fungal network (Enterocarpus, Aspergillus, Leucothecium, Peniophora, and Wallemia) of the fungal network which might suppress the most dominant pathogen, Plectosphaerella. In conclusion, biofumigation-derived soil microbiome alterations have the potential to lower plant stress under drought. [ABSTRACT FROM AUTHOR]

Marine macroalgae, which typically colonize coastal areas, are simple plant organisms. They live on rocks in coastal regions and are classified into red, brown, and green macroalgae. These algae are an important natural resource in agriculture due to their ability to enhance the structural, chemical, and biological properties of soil. Marine macroalgae can be used to produce various biocidal molecules that are effective in controlling plant pathogens. Much of the literature on marine macroalgae and their derivatives focuses primarily on the pharmaceutical field, while their use in agriculture is still considered secondary. However, various studies and experiments have demonstrated their potential to play a significant role in crop protection and enhancement. This review aims to highlight the various applications of macroalgae in plant production. It also emphasizes the biotechnological importance of marine macroalgae derivatives as biofertilizers, molecules for controlling insects and microorganisms, and as plant growth conditioners. Compounds from macroalgae, such as fatty acids, carotenoids, polyphenols, and carbohydrates, are being investigated for their fungicidal, antimicrobial, and antiviral effects against various plant pathogens. Beyond enhancing crop production, macroalgae can also be considered multifunctional bioinoculants suitable for use in organic farming. [ABSTRACT FROM AUTHOR]

Bacillus sp. G2112, an isolate from cucumber plants that inhibited plant pathogens, produces not only surfactins, iturins, and fengycins common to many Bacillus spp., but also a large variety of N-acyl-(depsi)peptides related to A-3302-B and nobilamides. Four known and fourteen previously unreported nobilamide peptides were characterized using high-resolution mass spectrometry, tandem mass spectrometry, and NMR. The stereochemistry of the amino acids of nobilamide peptides was determined using Marfey's method. The diversity of nobilamide peptides from Bacillus sp. G2112 resulted from the incorporation of different acyl groups and amino acids in the sequence. The peptides occur in linear or cyclic form. In addition, a truncated N-acetylpentapeptide was produced. Agar diffusion assays with selected nobilamide peptides against plant pathogens and human pathogens revealed that A-3302-B and its N-acyl homologs, A-3302-A and nobilamide J, exhibited powerful antibiotic activity (at 5 µg/hole) against Lysinibacillus sphaericus that can cause severe sepsis and bacteremia in patients. Moreover, nobilamide peptides from Bacillus sp. G2112 strongly promoted biofilm formation in the Gram-positive Mycobacterium aurum and Gram-negative pseudomonads. Structurally diverse nobilamides from Bacillus sp. G2112, whether linear or cyclic, penta and heptapeptides, induced biofilm formation, suggesting that the common N-acetyl-D-Phe-D-Leu-L-Phe-D-allo-Thr-L-Val amino acid sequence motif is important for the biofilm-inducing activity. [ABSTRACT FROM AUTHOR]

Simple Summary: The corn leafhopper, an invasive insect and vector of corn stunt spiroplasma, has been reported in multiple counties in Oklahoma. Corn stunt spiroplasma-infected corn leafhoppers were also confirmed in the state. The corn leafhopper, Dalbulus maidis (DeLong and Wolcott) (Hemiptera: Cicadellidae), is an invasive insect that can cause damage to maize (Zea mays L.) in two ways: by direct feeding and the transmission of several plant pathogens. Dalbulus maidis is an invasive and serious economic pest of maize that has spread from its center of origin in Mexico to the southernmost parts of the United States. Prior to 2024, corn leafhoppers had not been documented in Oklahoma, and their spread northward toward the United States corn belt is of significant concern. Here, we provide the first reports of the insect in maize in several Oklahoma counties. Insect specimens were collected at various commercial and experimental field sites by Oklahoma State University research and extension personnel. The identity of the insect species was validated through morphological and molecular taxonomy. The presence records for the corn leafhopper presented here provide valuable information for future monitoring and management efforts of this economically important pest and disease. [ABSTRACT FROM AUTHOR]

This review covers, for the first time, all methods based on the use of Aspergillus strains as biocontrol agents for the management of plant diseases caused by fungi and oomycetes. Atoxigenic Aspergillus strains have been screened in a variety of hosts, such as peanuts, maize kernels, and legumes, during the preharvest and postharvest stages. These strains have been screened against a wide range of pathogens, such as Fusarium, Phytophthora, and Pythium species, suggesting a broad applicability spectrum. The highest efficacies were generally observed when using non-toxigenic Aspergillus strains for the management of mycotoxin-producing Aspergillus strains. The modes of action included the synthesis of antifungal metabolites, such as kojic acid and volatile organic compounds (VOCs), secretion of hydrolytic enzymes, competition for space and nutrients, and induction of disease resistance. Aspergillus strains degraded Sclerotinia sclerotiorum sclerotia, showing high control efficacy against this pathogen. Collectively, although two Aspergillus strains have been commercialized for aflatoxin degradation, a new application of Aspergillus strains is emerging and needs to be optimized. [ABSTRACT FROM AUTHOR]

Velvet proteins, as well as the epigenetic regulator LaeA, are conserved in numerous fungal species, where, in response to environmental cues, they control several crucial cellular processes, including sexual and asexual morphogenesis, secondary metabolism, response to oxidative stress, and virulence. During the last two decades, knowledge of their mechanism of action as well as understanding their functional roles, has greatly increased, particularly in Aspergillus species. Research efforts from multiple groups followed, leading to the characterization of other Velvet and LaeA homologs in species of other fungal genera, including important opportunistic plant and animal pathogens. This review focuses mainly on the current knowledge of the role of Velvet and LaeA function in fungal pathogenesis. Velvet proteins and LaeA are unique to fungi, and for this reason, additional knowledge of these critical regulatory proteins will be important in the development of targeted control strategies to decrease the detrimental impact of fungal pathogens capable of causing disease in plants and animals. [ABSTRACT FROM AUTHOR]

Erwinia amylovora, the causative agent of fire blight, causes significant economic losses for farmers worldwide by inflicting severe damage to the production and quality of plants in the Rosaceae family. Historically, fire blight control has primarily relied on the application of copper compounds and antibiotics, such as streptomycin. However, the emergence of antibiotic-resistant strains and growing environmental concerns have highlighted the need for alternative control methods. Recently, there has been a growing interest in adopting bacteriophages (phages) as a biological control strategy. Phages have demonstrated efficacy against the bacterial plant pathogen E. amylovora, including strains that have developed antibiotic resistance. The advantages of phage therapy includes its minimal impact on microbial community equilibrium, the lack of a detrimental impact on plants and beneficial microorganisms, and its capacity to eradicate drug-resistant bacteria. This review addresses recent advances in the isolation and characterization of E. amylovora phages, including their morphology, host range, lysis exertion, genomic characterization, and lysis mechanisms. Furthermore, this review evaluates the environmental tolerance of E. amylovora phages. Despite their potential, E. amylovora phages face certain challenges in practical applications, including stability issues and the risk of lysogenic conversion. This comprehensive review examines the latest developments in the application of phages for controlling fire blight and highlights the potential of E. amylovora phages in plant protection strategies. [ABSTRACT FROM AUTHOR]

The aim of this study was to determine the activity of common thyme (Thymus vulgare L.), Greek oregano (Origanum vulgare L. ssp. hirtum), and common oregano (Origanum vulgare L. ssp. vulgare) essential oils (EOs) against selected phytopathogenic microorganisms in relation to their chemical profile. The EOs were obtained from the herbs of 2-year-old plants cultivated in the organic farming system in a temperate climate in Central Europe. The EOs' composition was determined by GC/MS and GC/FID. The investigated species were represented by the following three chemotypes: 'thymol' for common thyme, 'carvacrol' for Greek oregano, and mixed 'caryophyllene oxide + β-caryophyllene' for common oregano. The antimicrobial activity of the EOs was assessed based on minimum inhibitory concentration (MIC) and minimum bactericidal/fungicidal concentration (MBC/MFC) values. The plant pathogenic bacteria Pseudomonas syringae, Xanthomonas hortorum, Erwinia carotovora, and fungi: Fusarium culmorum, Alternaria alternata, Botrytis cinerea, Epicoccum purpurascens, Cladosporium cladosporioides, Phoma strasseri, and Pythium debaryanum were tested. The EOs revealed a stronger inhibitory effect against fungal growth in comparison to bacterial growth (MIC: 0.016–2 µL/mL for fungi and 0.125–4 µL/mL for bacteria). Common thyme and Greek oregano EOs indicated stronger antimicrobial power than common oregano EO. These results were associated with the chemical profile of the analysed EOs. The growth of examined bacteria and fungi strains (in particular, X. hortorum, F. culmorum, and P. debaryanum) were negatively correlated with the content of phenolic monoterpenes and monoterpene hydrocarbons. Among the tested strains, P. strasseri turned out to be the most sensitive (MIC 0.016 µL/mL) and E. carotovora the most resistant (MIC 0.250–4 µL/mL) to all investigated EOs. [ABSTRACT FROM AUTHOR]

Bacteria of the genus Pseudomonas are ubiquitous on Earth due to their great metabolic versatility and adaptation to fluctuating environments and different hosts. Some groups are important animal/human and plant pathogens, whereas others are studied for their biotechnological applications, including bioremediation, biological control of phytopathogens and plant growth promotion. Notably, their adaptability is mediated by various signal transduction systems, with the post‐transcriptional Gac‐Rsm cascade playing a key role. This pervasive Pseudomonas pathway controls major transitions at the population level, such as motile/sessile lifestyle, primary/secondary metabolism or replicative/infective behaviour. A hallmark of the Gac‐Rsm cascade is the participation of small, regulatory, non‐coding RNAs of the Rsm clan. These RNAs are synthetised in response to cell‐density‐dependent autoinducer signals channelled through the GacS/GacA two‐component system, and they counteract, by molecular mimicry, the translational control that RNA‐binding proteins of the RsmA family exert over hundreds of mRNAs. Rsm RNAs have been investigated in a few Pseudomonas model species, evidencing the presence of a variable number and families of genes depending on the taxonomic clade. However, the global picture of the distribution of these riboregulators at the genus level was unknown until now. We have undertaken a comprehensive survey and annotation of the vast array of gene sequences encoding members of the Rsm RNA clan in 245 complete genomes that cover 28 phylogenomic clades across the entire genus. The properties of the different families of rsm genes, their phylogenetic radiation, as well as the features of their promoters and adjacent regions, are discussed. The novel insights presented in our manuscript will significantly boost research on the biology of these prevalent RNAs in understudied species of the genus Pseudomonas and closely related genera. [ABSTRACT FROM AUTHOR]

Maize production and quality are affected by infection with plant pathogens. One of the maize's essential and main diseases is downy mildew caused by Peronosclerospora spp. Downy mildew is a limiting factor in increasing production and can reduce production by 80-100%. It is because the affected plant cannot produce cobs. Pathogens obtain nutrients from the host cell, which can kill the cell and damage the surrounding tissues, resulting in visible downy mildew symptoms. Boron (B) plays a role in forming phloem, increasing the fruit's number, weight, bunch weight, and diameter. The primary function of B at the molecular level is the cross-linking of pectin in the plant cell wall. Ramnogalacturonan II (RG II) is a pectic polysaccharide that contributes to the mechanical strength and properties of the primary wall cross-linked by borate diesters. Phosphorus (P) controls the downsides in the greenhouse and field conditions. This study aims to measure changes in chlorophyll index, P and B uptakes in downy mildew affected plants. The field experiment used a group randomized design with six natural phosphate (FA) application treatments and four groups of borax doses as replicates. The results showed that the downy mildew decreased the chlorophyll index of the leaves at different levels of attack. The results of P concentration according to the position of healthy plant leaves were significantly different due to P treatment. In contrast to concentration B, there is no real difference. P and B uptake results in downy mildew-infested plants showed a significant difference only in P uptake in leaves with 1 FA treatment. [ABSTRACT FROM AUTHOR]

Continuous cropping is a common cultivation practice in lavender cultivation, and the structure of the soil microbial community is one of the main reasons affecting the continuous cropping disorder in lavender; however, the relationship between the number of years of cultivation and inter-root microbial composition has not yet been investigated; using Illumina high-throughput sequencing we detected fungal community structure of rhizosphere soil under 1 (L1), 3 (L3), 5 (L5) and 0 (L0) years' of lavender cultivation in Yili, Xinjiang China. The results showed that with the extension of planting years, the physical-chemical characteristics of the soil shifted, and the diversity of the fungal communities shrank, the abundance and richness of species decreased and then increased, and the phylogenetic diversity increased, The structure of the soil fungal communities varied greatly. At phylum level, dominant fungal phyla were Ascomycetes, Basidiomycetes, etc. At genus level, dominant genera were Gibberella, Mortierella, etc, whose absolute abundance all increased with increasing planting years (P < 0.05); redundancy analysis showed that thesoil physicochemical characteristics significantly correlated with dominant bacterial genera. The FUN Guild prediction showed that six groups of plant pathogens and plant saprotrophs changed significantly (P < 0.05), the amount of harmful bacteria in the soil increased while the amount of arbuscular mycorrhizal fungui (AMF) decreased, leading to a continuous cropping obstacle of lavender. The findings of this study provida theoretical foundation for the management of continuous cropping and the prevention fungus-related diseases in lavender. [ABSTRACT FROM AUTHOR]

Summary: All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil‐borne microbial communities in driving endogenous fluctuations of plant populations.We combined a unique, 35‐yr long abundance data of 11 common plant species from a species‐rich mountain meadow with development of their soil microbiome (pathogenic fungi, arbuscular mycorrhizal fungi and oomycetes) observed during 4 yr of experimental cultivation in monocultures.Plant species which abundance fluctuated highly in the field (particularly legumes) accumulated plant pathogens in their soil mycobiome. We also identified increasing proportion of mycoparasitic fungi under highly fluctuating legume species, which may indicate an adaptation of these species to mitigate the detrimental effects of pathogens.Our study documented that long‐term fluctuations in the abundance of plant species in grassland communities can be explained by the accumulation of plant pathogens in plant–soil microbiome. By contrast, we found little evidence of the role of mutualists in plant population fluctuations. These findings offer new insights for understanding mechanisms driving both long‐term vegetation dynamics and patterns of species coexistence and richness. [ABSTRACT FROM AUTHOR]