Search

Hemipteran insects transmit viruses when infesting plants, during which vectors activate salicylic acid (SA)-regulated antiviral defenses. How vector-borne plant viruses circumvent these antiviral defenses is largely unexplored. During co-infections of begomoviruses and betasatellites in plants, betasatellite-encoded βC1 proteins interfere with SA signaling and reduce the activation of antiviral resistance. βC1 inhibits SA-induced degradation of NbNPR3 (Nicotiana benthamiana nonexpressor of pathogenesis-related genes 3), a negative regulator of SA signaling. βC1 does not bind directly to NbNPR3, but regulates NbNPR3 degradation via heat shock protein 90s (NbHSP90s). NbHSP90s bind to both NbNPR3 and βC1 and suppress SA signaling. This viral success strategy appears to be conserved as it is also documented for viral proteins encoded by two aphid-borne viruses. Our findings reveal an exquisite mechanism that facilitates the persistence of vector-borne plant viruses and provide important insights into the intricacies of the virus life cycle.

This article is a Commentary on Yu et al. (2024), 244: 1024–1040.

Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters (aux clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.

Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease esca. We present the genomes of 4 species associated with esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing. The genomic and functional comparisons identified potential virulence factors, suggesting their roles in disease development. Similar to other white-rot fungi known for their ability to degrade lignocellulosic substrates, these 4 genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in esca symptoms and host resistance.

UNLABELLED: To gain insights into the diversity of Pseudomonas syringae sensu lato affecting sweet cherry in California, we sequenced and analyzed the phylogenomic and genomic architecture of 86 fluorescent pseudomonads isolated from symptomatic and asymptomatic cherry tissues. Fifty-eight isolates were phylogenetically placed within the P. syringae species complex and taxonomically classified into five genomospecies: P. syringae pv. syringae, P. syringae, Pseudomonas cerasi, Pseudomonas viridiflava, and A. We annotated components of the type III secretion system and phytotoxin-encoding genes and correlated the data with pathogenicity phenotypes. Intact probable regulatory protein HrpR was annotated in the genomic sequences of all isolates of P. syringae pv. syringae, P. syringae, P. cerasi, and A. Isolates of P. viridiflava had atypical probable regulatory protein HrpR. Syringomycin and syringopeptin-encoding genes were annotated in isolates of all genomospecies except for A and P. viridiflava. All isolates of P. syringae pv. syringae caused cankers, leaf spots, and fruit lesions in the field. In contrast, all isolates of P. syringae and P. cerasi and some isolates of P. viridiflava caused only cankers. Isolates of genomospecies A could not cause any symptoms suggesting phytotoxins are essential for pathogenicity. On detached immature cherry fruit pathogenicity assays, isolates of all five genomospecies produced symptoms (black-dark brown lesions). However, symptoms of isolates of genomospecies A were significantly (P < 0.01) less severe than those of other genomospecies. We also mined for genes conferring resistance to copper and kasugamycin and correlated these data with in vitro antibiotic sensitivity tests. IMPORTANCE: Comprehensive identification of phytopathogens and an in-depth understanding of their genomic architecture, particularly virulence determinants and antibiotic-resistant genes, are critical for several practical reasons. These include disease diagnosis, improved knowledge of disease epidemiology, pathogen diversity, and determination of the best possible management strategies. In this study, we provide the first report of the presence and pathogenicity of genomospecies Pseudomonas cerasi and Pseudomonas viridiflava in California sweet cherry. More importantly, we report a relatively high level of resistance to copper among the population of Pseudomonas syringae pv. syringae (47.5%). This implies copper cannot be effectively used to control bacterial blast and bacterial canker of sweet cherries. On the other hand, no isolates were resistant to kasugamycin, an indication that kasugamycin could be effectively used for the control of bacterial blast and bacterial canker. Our findings are important to improve the management of bacterial blast and bacterial canker of sweet cherries in California.

Vector-borne bacterial pathogens cause devastating plant diseases that cost billions of dollars in crop losses worldwide. These pathogens have evolved to be host- and vector-dependent, resulting in a reduced genome size compared to their free-living relatives. All known vector-borne bacterial plant pathogens belong to four different genera: Candidatus Liberibacter, Candidatus Phytoplasma, Spiroplasma and Xylella. To protect themselves against pathogens, plants have evolved pattern recognition receptors that can detect conserved pathogen features as non-self and mount an immune response. To gain an understanding of how vector-borne pathogen features are perceived in plants, we investigated three proteinaceous features derived from cold shock protein (csp22), flagellin (flg22) and elongation factor Tu (elf18) from vector-borne bacterial pathogens as well as their closest free-living relatives. In general, vector-borne pathogens have fewer copies of genes encoding flagellin and cold shock protein compared to their closest free-living relatives. Furthermore, epitopes from vector-borne pathogens were less likely to be immunogenic compared to their free-living counterparts. Most Liberibacter csp22 and elf18 epitopes do not trigger plant immune responses in tomato or Arabidopsis. Interestingly, csp22 from the citrus pathogen Candidatus Liberibacter asiaticus triggers immune responses in solanaceous plants, while csp22 from the solanaceous pathogen Candidatus Liberibacter solanacearum does not. Our findings suggest that vector-borne plant pathogenic bacteria evolved to evade host recognition.

Zymoseptoria tritici is the most economically significant fungal pathogen of wheat in Europe. However, despite the importance of this pathogen, the molecular interactions between pathogen and host during infection are not well understood. Herein, we describe the use of two libraries of cloned Z. tritici effectors that were screened to identify effector candidates with putative pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI)-suppressing activity. The effectors from each library were transiently expressed in Nicotiana benthamiana, and expressing leaves were treated with bacterial or fungal PAMPs to assess the effectors ability to suppress reactive oxygen species (ROS) production. From these screens, numerous effectors were identified with PTI-suppressing activity. In addition, some effectors were able to suppress cell death responses induced by other Z. tritici secreted proteins. We used structural prediction tools to predict the putative structures of all of the Z. tritici effectors and used these predictions to examine whether there was enrichment of specific structural signatures among the PTI-suppressing effectors. From among the libraries, multiple members of the killer protein-like 4 (KP4) and killer protein-like 6 (KP6) effector families were identified as PTI suppressors. This observation is intriguing, as these protein families were previously associated with antimicrobial activity rather than virulence or host manipulation. This data provides mechanistic insight into immune suppression by Z. tritici during infection and suggests that, similar to biotrophic pathogens, this fungus relies on a battery of secreted effectors to suppress host immunity during early phases of colonization.

The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.

Bacterial biofilm formation and attachment to hosts are mediated by carbohydrate-binding lectins, exopolysaccharides, and their interactions in the extracellular matrix (ECM). During tomato infection Ralstonia pseudosolanacearum (Rps) GMI1000 highly expresses three lectins: LecM, LecF, and LecX. The latter two are uncharacterized. We evaluated the roles in bacterial wilt disease of LecF, a fucose-binding lectin, LecX, a xylose-binding lectin, and the Rps exopolysaccharide EPS I. Interestingly, single and double lectin mutants attached to tomato roots better and formed more biofilm under static conditions in vitro. Consistent with this finding, static bacterial aggregation was suppressed by heterologous expression of lecFGMI1000 and lecXGMI1000 in other Ralstonia strains that naturally lack these lectins. Crude ECM from a ΔlecF/X double mutant was more adhesive than the wild-type ECM, and LecF and LecX increased Rps attachment to ECM. The enhanced adhesiveness of the ΔlecF/X ECM could explain the double mutants hyper-attachment in static conditions. Unexpectedly, mutating lectins decreased Rps attachment and biofilm viscosity under shear stress, which this pathogen experiences in plant xylem. LecF, LecX, and EPS I were all essential for biofilm development in xylem fluid flowing through cellulose-coated microfluidic channels. These results suggest that under shear stress, LecF and LecX increase Rps attachment by interacting with the ECM and plant cell wall components like cellulose. In static conditions such as on root surfaces and in clogged xylem vessels, the same lectins suppress attachment to facilitate pathogen dispersal. Thus, Rps lectins have a dual biological function that depends on the physical environment.

Plants produce reactive oxygen species (ROS) upon infection, which typically trigger defence mechanisms and impede pathogen proliferation. Root-knot nematodes (RKNs, Meloidogyne spp.) represent highly detrimental pathogens capable of parasitizing a broad spectrum of crops, resulting in substantial annual agricultural losses. The involvement of ROS in RKN parasitism is well acknowledged. In this study, we identified a novel effector from Meloidogyne incognita, named CATLe, that contains a conserved catalase domain, exhibiting potential functions in regulating host ROS levels. Phylogenetic analysis revealed that CATLe is conserved across RKNs. Temporal and spatial expression assays showed that the CATLe gene was specifically up-regulated at the early infection stages and accumulated in the subventral oesophageal gland cells of M. incognita. Immunolocalization demonstrated that CATLe was secreted into the giant cells of the host plant during M. incognita parasitism. Transient expression of CATLe significantly dampened the flg22-induced ROS production in Nicotiana benthamiana. In planta assays confirmed that M. incognita can exploit CATLe to manipulate host ROS levels by directly degrading H2O2. Additionally, interfering with expression of the CATLe gene through double-stranded RNA soaking and host-induced gene silencing significantly attenuated M. incognita parasitism, highlighting the important role of CATLe. Taken together, our results suggest that RKNs can directly degrade ROS products using a functional catalase, thereby manipulating host ROS levels and facilitating parasitism.

Botryosphaeriaceae species are the major causal agents of walnut dieback worldwide, along with Diaporthe species. Botryosphaeria dothidea and Neofusicoccum parvum are the only two Botryosphaeriaceae species associated with this recently emergent disease in France, and little is known about their diversity, structure, origin and dispersion in French walnut orchards. A total of 381 isolates of both species were genetically typed using a sequence-based microsatellite genotyping (SSR-seq) method. This analysis revealed a low genetic diversity and a high clonality of these populations, in agreement with their clonal mode of reproduction. The genetic similarity among populations, regardless of the tissue type and the presence of symptoms, supports the hypothesis that these pathogens can move between fruits and twigs and display latent pathogen lifestyles. Contrasting genetic patterns between N. parvum populations from Californian and Spanish walnut orchards and the French ones suggested no conclusive evidence for pathogen transmission from infected materials. The high genetic similarity with French vineyards populations suggested instead putative transmission between these hosts, which was also observed with B. dothidea populations. Overall, this study provides critical insight into the epidemiology of two important pathogens involved in the emerging dieback of French walnut orchards, including their distribution, potential to mate, putative origin and disease pathways.

The crosstalk between clathrin-mediated endocytosis (CME) and the autophagy pathway has been reported in mammals; however, the interconnection of CME with autophagy has not been established in plants. Here, we report that the Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopies Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants in both autoimmunity and nutrient sensitivity. Accordingly, the autophagy pathway is significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation, and degradation of GFP-ATG8h is significantly reduced in the clc2-1 clc3-1 mutant. Notably, simultaneous knockout of ATG8h and ATG8i by CRISPR-Cas9 results in enhanced resistance against Golovinomyces cichoracearum, supporting the functional relevance of the CLC2-ATG8h/8i interactions. In conclusion, our results reveal a link between the function of CLCs and the autophagy pathway in Arabidopsis.

Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Candidatus Liberibacter asiaticus (CLas), is vectored by Diaphorina citri, known as the Asian citrus psyllid (ACP). Understanding the details of CLas infection in HLB disease has been hindered by its Candidatus nature and the inability to confidently detect it in diseased trees during the asymptomatic stage. To identify early changes in citrus metabolism in response to inoculation of CLas using its natural psyllid vector, leaves from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck) trees were exposed to CLas-positive ACP or CLas-negative ACP and longitudinally analyzed using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry; data available in Dryad: 10.25338/B83H1Z), and metabolomics (proton nuclear magnetic resonance). At 4 weeks postexposure (wpe) to psyllids, the initial HLB plant response was primarily to the ACP and, to a lesser extent, the presence or absence of CLas. Additionally, analysis of 4, 8, 12, and 16 wpe identified 17 genes and one protein as consistently differentially expressed between leaves exposed to CLas-positive ACP versus CLas-negative ACP. This study informs identification of early detection molecular targets and contributes to a broader understanding of vector-transmitted plant pathogen interactions.

Saponins are plant secondary metabolites comprising glycosylated triterpenoids, steroids or steroidal alkaloids with a broad spectrum of toxicity to microbial pathogens and pest organisms that contribute to basal plant defense to biotic attack. Secretion of glycosyl hydrolases that enzymatically convert saponins into less toxic products was thus far the only mechanism reported to enable fungal pathogens to colonize their saponin-containing host plant(s). We studied the mechanisms that the fungus Botrytis cinerea utilizes to be tolerant to well-characterized, structurally related saponins from tomato and Digitalis purpurea. By gene expression studies, comparative genomics, enzyme assays and testing a large panel of fungal (knockout and complemented) mutants, we unraveled four distinct cellular mechanisms that participate in the mitigation of the toxic activity of these saponins and in virulence on saponin-producing host plants. The enzymatic deglycosylation that we identified is novel and unique to this fungus-saponin combination. The other three tolerance mechanisms operate in the fungal membrane and are mediated by protein families that are widely distributed in the fungal kingdom. We present a spatial and temporal model on how these mechanisms jointly confer tolerance to saponins and discuss the repercussions of these findings for other plant pathogenic fungi, as well as human pathogens.

BACKGROUND: Sclerotinia spp. are generalist fungal pathogens, infecting over 700 plant hosts worldwide, including major crops. While host resistance is the most sustainable and cost-effective method for disease management, complete resistance to Sclerotinia diseases is rare. We recently identified soft basal stem as a potential susceptibility factor to Sclerotinia minor infection in lettuce (Lactuca sativa) under greenhouse conditions. RESULTS: Analysis of stem and root cell wall composition in five L. sativa and one L. serriola accessions with varying growth habits and S. minor resistance levels revealed strong association between hemicellulose constituents, lignin polymers, disease phenotypes, and basal stem mechanical strength. Accessions resistant to basal stem degradation consistently exhibited higher levels of syringyl, guaiacyl, and xylose, but lower levels of fucose in stems. These findings suggest that stem cell wall polymers recalcitrant to breakdown by lignocellulolytic enzymes may contribute to stem strength-mediated resistance against S. minor. CONCLUSIONS: The lignin content, particularly guaiacyl and syringyl, along with xylose could potentially serve as biomarkers for identifying more resistant lettuce accessions and breeding lines. Basal stem degradation by S. minor was influenced by localized microenvironment conditions around the stem base of the plants.

BackgroundSoybean cyst nematodes (SCN) as animal parasites of plants are not usually interested in killing the host but are rather focused on completing their life cycle to increase population, resulting in substantial yield losses. Remarkably, some agricultural soils after long-term crop monoculture show a significant decline in SCN densities and suppress disease in a sustainable and viable manner. However, relatively little is known about the microbes and mechanisms operating against SCN in such disease-suppressive soils.ResultsGreenhouse experiments showed that suppressive soils (S) collected from two provinces of China and transplantation soils (CS, created by mixing 10% S with 90% conducive soils) suppressed SCN. However, SCN suppressiveness was partially lost or completely abolished when S soils were treated with heat (80 °C) and formalin. Bacterial community analysis revealed that the specific suppression in S and CS was mainly associated with the bacterial phylum Bacteroidetes, specifically due to the enrichment of Chitinophaga spp. and Dyadobacter sp., in the cysts. SCN cysts colonized by Chitinophaga spp. showed dramatically reduced egg hatching, with unrecognizable internal body organization of juveniles inside the eggshell due to chitinase activity. Whereas, Dyadobacter sp. cells attached to the surface coat of J2s increased soybean resistance against SCN by triggering the expression of defence-associated genes. The disease-suppressive potential of these bacteria was validated by inoculating them into conducive soil. The Dyadobacter strain alone or in combination with Chitinophaga strains significantly decreased egg densities after one growing cycle of soybeans. In contrast, Chitinophaga strains alone required more than one growing cycle to significantly reduce SCN egg hatching and population density.ConclusionThis study revealed how soybean monoculture for decades induced microbiota homeostasis, leading to the formation of SCN-suppressive soil. The high relative abundance of antagonistic bacteria in the cyst suppressed the SCN population both directly and indirectly. Because uncontrolled proliferation will likely lead to quick demise due to host population collapse, obligate parasites like SCN may have evolved to modulate virulence/proliferation to balance these conflicting needs. Video Abstract.

The unculturable bacterium 'Candidatus Liberibacter solanacearum' (CLso) is responsible for a growing number of emerging crop diseases. However, we know little about the diversity and ecology of CLso and its psyllid vectors outside of agricultural systems, which limits our ability to manage crop disease and understand the impacts this pathogen may have on wild plants in natural ecosystems. In North America, CLso is transmitted to crops by the native potato psyllid (Bactericera cockerelli). However, the geographic and host plant range of the potato psyllid and CLso beyond the borders of agriculture are not well understood. A recent study of historic herbarium specimens revealed that a unique haplotype of CLso was present infecting populations of the native perennial Solanum umbelliferum in California decades before CLso was first detected in crops. We hypothesized that this haplotype and other potentially novel CLso variants are still present in S. umbelliferum populations. To test this, we surveyed populations of S. umbelliferum in Southern California for CLso and potato psyllid vectors. We found multiple haplotypes of CLso and the potato psyllid associated with these populations, with none of these genetic variants having been previously reported in California crops. These results suggest that CLso and its psyllid vectors are much more widespread and diverse in North American natural plant communities than suggested by data collected solely from crops and weeds in agricultural fields. Further characterization of these apparently asymptomatic haplotypes will facilitate comparison with disease-causing variants and provide insights into the continued emergence and spread of CLso.

Plant pathogenic bacteria often have a narrow host range, which can vary among different isolates within a population. Here, we investigated the host range of the tomato pathogen Clavibacter michiganensis (Cm). We determined the genome sequences of 40 tomato Cm isolates and screened them for pathogenicity on tomato and eggplant. Our screen revealed that out of the tested isolates, five were unable to cause disease on any of the hosts, 33 were exclusively pathogenic on tomato, and two were capable of infecting both tomato and eggplant. Through comparative genomic analyses, we identified that the five non-pathogenic isolates lacked the chp/tomA pathogenicity island, which has previously been associated with virulence in tomato. In addition, we found that the two eggplant-pathogenic isolates encode a unique allelic variant of the putative serine hydrolase chpG (chpGC), an effector that is recognized in eggplant. Introduction of chpGC into a chpG inactivation mutant in the eggplant-non-pathogenic strain Cm101, failed to complement the mutant, which retained its ability to cause disease in eggplant and failed to elicit hypersensitive response (HR). Conversely, introduction of the chpG variant from Cm101 into an eggplant pathogenic Cm isolate (C48), eliminated its pathogenicity on eggplant, and enabled C48 to elicit HR. Our study demonstrates that allelic variation in the chpG effector gene is a key determinant of host range plasticity within Cm populations.

Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.

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.

Autophagy in eukaryotes functions to maintain homeostasis by degradation and recycling of long-lived and unwanted cellular materials. Autophagy plays important roles in pathogenicity of various fungal pathogens, suggesting that autophagy is a novel target for development of antifungal compounds. Here, we describe bioluminescence resonance energy transfer (BRET)-based high-throughput screening (HTS) strategy to identify compounds that inhibit fungal ATG4 cysteine protease-mediated cleavage of ATG8 that is critical for autophagosome formation. We identified ebselen (EB) and its analogs ebselen oxide (EO) and 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PT) as inhibitors of fungal pathogens Botrytis cinerea and Magnaporthe oryzae ATG4-mediated ATG8 processing. The EB and its analogs inhibit spore germination, hyphal development, and appressorium formation in Ascomycota pathogens, B. cinerea, M. oryzae, Sclerotinia sclerotiorum and Monilinia fructicola. Treatment with EB and its analogs significantly reduced fungal pathogenicity. Our findings provide molecular insights to develop the next generation of antifungal compounds by targeting autophagy in important fungal pathogens.

Theodor (Ted) Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the Plant Virology Laboratory, Agricultural Research Service, USDA, in Beltsville. He coined the name viroid and defined viroids important features like the infectivity of naked single-stranded RNA without protein-coding capacity. During scientific meetings in the 1970s and 1980s, viroids were often discussed at conferences together with other subviral pathogens. This term includes what are now called satellite RNAs and prions. Satellite RNAs depend on a helper virus and have linear or, in the case of virusoids, circular RNA genomes. Prions, proteinaceous infectious particles, are the agents of scrapie, kuru and some other diseases. Many satellite RNAs, like viroids, are non-coding and exert their function by thermodynamically or kinetically controlled folding, while prions are solely host-encoded proteins that cause disease by misfolding, aggregation and transmission of their conformations into infectious prion isoforms. In this memorial, we will recall the work of Ted Diener on subviral pathogens.

BACKGROUND: Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen Cladosporium fulvum, which is the first fungal plant pathogen from which avirulence (Avr) genes were ever cloned and in which loss of Avr genes is often reported as a means of overcoming recognition by cognate tomato Cf resistance genes. A recent near-complete reference genome assembly of C. fulvum isolate Race 5 revealed a compartmentalized genome architecture and the presence of an accessory chromosome, thereby creating a basis for studying genome plasticity in fungal plant pathogens and its impact on avirulence genes. RESULTS: Here, we obtained near-complete genome assemblies of four additional C. fulvum isolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate Race 5 revealed high levels of synteny and colinearity, which extended to the density and distribution of repetitive elements and of repeat-induced point (RIP) mutations across homologous chromosomes. Nonetheless, structural variations, likely mediated by transposable elements and effecting the deletion of the avirulence genes Avr4E, Avr5, and Avr9, were also identified. The isolates further shared a core set of 13 chromosomes, but two accessory chromosomes were identified as well. Accessory chromosomes were significantly smaller in size, and one carried pseudogenized copies of two effector genes. Whole-genome alignments further revealed genomic islands of near-zero nucleotide diversity interspersed with islands of high nucleotide diversity that co-localized with repeat-rich regions. These regions were likely generated by RIP, which generally asymmetrically affected the genome of C. fulvum. CONCLUSIONS: Our results reveal new evolutionary aspects of the C. fulvum genome and provide new insights on the importance of genomic structural variations in overcoming host resistance in fungal plant pathogens.

The Asian Citrus Psyllid (ACP), Diaphorina citri, is a vector of the pathological bacterium Candidatus Liberibacter asiaticus (CLas), which causes the most devastating disease to the citrus industry worldwide, known as greening or huanglongbing (HLB). Earlier field tests with an acetic acid-based lure in greening-free, Valencia citrus orange groves in California showed promising results. The same type of lures tested in São Paulo, Brazil, showed unsettling results. During the unsuccessful trials, we noticed a relatively large proportion of females in the field, ultimately leading us to test field-collected males and females for Wolbachia and CLas. The results showed high rates of Wolbachia and CLas infection in field populations. We then compared the olfactory responses of laboratory-raised, CLas-free, and CLas-infected males to acetic acid. As previously reported, CLas-uninfected males responded to acetic acid at 1 µg. Surprisingly, CLas-infected males required 50 × higher doses of the putative sex pheromone, thus explaining the failure to capture CLas-infected males in the field. CLas infection was also manifested in electrophysiological responses. Electroantennogram responses from CLas-infected ACP males were significantly higher than those obtained with uninfected males. To the best of our knowledge, this is the first report of a pathogen infection affecting a vectors response to a sex attractant.

BackgroundColletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.ResultsHere we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.ConclusionsThese results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.

A survey conducted in the 1920s, prior to the chestnut blight, indicated that chestnuts and oaks were codominant canopy species in White Oak Canyon, Shenandoah National Park, Virginia. A second survey in 1977 suggested that chestnuts were being replaced by tree species present before the blight, particularly oaks. In 2021, we resurveyed the 10 sites included in our 1977 survey and also recorded canopy and understory trees that grew above remnant chestnut sprouts. The canopy changed more substantially during the second interval (since 1977). Birch and maples were now more abundant. Hemlock declined, and oaks were less common in the canopy. In general, the trees considered as early to mid-successional have replaced oaks and hemlock. Chestnut sprouts have become much less common since 1977, presumably as repeated cycles of diebacks have weakened rootstocks. Those sites where chestnut sprouts have persisted until 2021 differed from neighboring sites without them. Chestnut sprouts were rare in sites with birch and hemlock; chestnut has persisted in locations with red oaks in the canopy and with few other understory competitors. This survey has been conducted over a longer time interval than previous studies that asked similar questions and our results suggest that changes to the forest composition following the loss of the American chestnut may be greater than previously recognized although the relative contribution of losing this codominant species is unclear.

Tomato spotted wilt orthotospovirus (TSWV) causes substantial economic loss to tomato production, and the Sw-5b resistance gene is widely deployed for management. Here, we show (i) the emergence of resistance-breaking (RB) TSWV strains in processing and fresh market tomato production in California over the past ten years, and (ii) evolutionary relationships with RB strains from other areas. A specific RT-PCR test was used to show the C118Y RB strain that emerged in Fresno County in 2016 quickly became predominant in the central production area and remained so through this study. In 2021, the C118Y strain was detected in the Northern production area, and was predominant in 2022. However, in 2023, the C118Y strain was unexpectedly detected in fewer spotted wilt samples from resistant varieties. This was due to emergence of the T120N RB strain, previously known to occur in Spain. A specific RT-PCR test was developed and used to show that the T120N RB strain was predominant in Colusa and Sutter counties (detected in 75-80% of samples), and detected in ~50% of samples from Yolo County. Pathogenicity tests confirmed California isolates of the T120N strain infected Sw-5b tomato varieties and induced severe symptoms. Another RB strain, C118F, was associated with spotted wilt samples of Sw-5 varieties from fresh market tomato production in southern California. Phylogenetic analyses with complete NSm sequences revealed that the C118Y and T120N RB strains infecting resistant processing tomato in California emerged locally, whereas those from fresh market production were more closely related to isolates from Mexico. Thus, widespread deployment of this single dominant resistance gene in California has driven the local emergence of multiple RB strains in different tomato production areas and types. These results further emphasize the need for ongoing monitoring for RB strains, and identification of sources of resistance to these strains.

The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.

Summary Crop diseases cause significant quality and yield losses to global crop products each year and are heavily controlled by chemicals along with very limited antibiotics composed of small molecules. However, these methods often result in environmental pollution and pest resistance, necessitating the development of new bio‐controlling products to mitigate these hazards. To identify effective antimicrobial peptides (AMPs) considered as potential sources of future antibiotics, AMPs were screened from five bacterial strains showing antagonism against a representative phytopathogenic fungus (Rhizoctonia Solani) through the Bacillus subtilis expression system, which has been developed for identifying bacterial AMPs by displaying autolysis morphologies. A total of 5000 colonies were screened, and five displaying autolysis morphologies showed antagonism against R. solani. A novel AMP with the strongest antagonism efficiency was determined and tentatively named HR2‐7, which is composed of 24 amino acids with an alpha‐helical structure. HR2‐7 has strong and broad‐spectrum antimicrobial activity, tested against 10 g‐positive and ‐negative bacteria and four phytopathogenic fungi by contact culture in plates with minimal lethal concentrations of 4.0 μM. When applied as purified peptide or in fermented B. subtilis culture solution, HR2‐7 showed strong controlling efficiency on plants against diverse fungal and bacterial pathogens. Based on current understanding, HR2‐7 is recognized as the first AMP derived from an agricultural antagonistic bacterium. It exhibits wide‐ranging and notable antimicrobial efficacy, offering a supplementary approach for managing plant diseases, in addition to conventional chemical pesticides and antibiotics. [ABSTRACT FROM AUTHOR]

Climate change is reshaping the interactions between plants and pathogens, exerting profound effects on global agricultural systems. Elevated tropospheric ozone levels due to climate change hinder plant photosynthesis and increase vulnerability to biotic invasion. The prevailing atmospheric conditions, including temperature and humidity, profoundly influence fungal pathogenesis, as each stage of a pathogen's life cycle is intricately linked to temperature variations. Likewise, climate change alters bacterial behaviour, fostering increased production of extracellular polysaccharides by plant‐pathogenic bacteria in warmer temperatures. Heat‐adapted bacteria, such as Burkholderia glumea and Ralstonia solanacearum, are emerging as significant global threats as temperature rise. Viruses, too, respond dynamically to climate shifts, with certain species favouring warmer climates for replication, resulting in expanded geographical ranges and modified transmission patterns. Nematodes, formidable constraints in crop production, exhibit temperature‐dependent life cycles and would have potentially accelerated proliferation and distribution as global warming progresses. Molecular‐level changes in pathogenesis, induced by temperature fluctuations, influence various pathogens, thereby impacting their virulence and interactions with host plants. Modelling studies predict changes in disease risks and distributions under future climate scenarios, highlighting the necessity of integrating climate data into crop disease models for accurate forecasts. Mechanistic and observational models illustrate pathogen behaviours amidst changing environmental conditions, providing crucial insights into future disease dynamics. In addition, controlled experiments study disease responses under simulated climate scenarios, underscoring the urgency for comprehensive research to devise effective resistance strategies against severe plant diseases. [ABSTRACT FROM AUTHOR]

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), is a foliar disease of wheat (Triticum aestivum) that adversely affects both grain yield and quality. Growing resistant cultivars offers an effective and environmentally sustainable solution to managing PM. However, relying on the same genetic source of resistance can lead to resistance breakdown as Bgt isolates rapidly evolve. To mitigate this, identifying novel resistance sources is crucial. In this study, 225 diverse wheat genotypes were evaluated at adult plant stage in disease nurseries over the three crop seasons (2018/2019, 2019/2020 and 2020/2021). Using disease and genotyping data from 12,160 single‐nucleotide polymorphism (SNP) markers, a genome‐wide association study (GWAS) was conducted to identify novel resistance loci. We identified 22 marker loci significantly (at p < 0.005) associated with PM resistance, distributed across 14 wheat chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 5D, 6A, 7A and 7B). Of these, seven loci overlap with previously identified regions, while the remaining 15 loci represent novel regions reported for the first time in this study. The identified SNP markers have significant potential for wheat breeding programmes, as they can accelerate the development of PM‐resistant cultivars through marker‐assisted selection. [ABSTRACT FROM AUTHOR]

Introduction: In response to the current mainstream deep learning detection methods with a large number of learned parameters and the complexity of apple leaf disease scenarios, the paper proposes a lightweight method and names it LCGSC-YOLO. This method is based on the LCNet(A Lightweight CPU Convolutional Neural Network) and GSConv(Group Shuffle Convolution) module modified YOLO(You Only Look Once) framework. Methods: Firstly, the lightweight LCNet is utilized to reconstruct the backbone network, with the purpose of reducing the number of parameters and computations of the model. Secondly, the GSConv module and the VOVGSCSP (Slim-neck by GSConv) module are introduced in the neck network, which makes it possible to minimize the number of model parameters and computations while guaranteeing the fusion capability among the different feature layers. Finally, coordinate attention is embedded in the tail of the backbone and after each VOVGSCSP module to improve the problem of detection accuracy degradation issue caused by model lightweighting. Results: The experimental results show the LCGSC-YOLO can achieve an excellent detection performance with mean average precision of 95.5% and detection speed of 53 frames per second (FPS) on the mixed datasets of Plant Pathology 2021 (FGVC8) and AppleLeaf9. Discussion: The number of parameters and Floating Point Operations (FLOPs) of the LCGSC-YOLO are much less thanother related comparative experimental algorithms. [ABSTRACT FROM AUTHOR]

The study investigated watermelon diseases characterized by contrasting climatic conditions in the Sylhet and Natore Districts of Bangladesh. Sylhet experiences lower temperatures and high rainfall, while Natore has higher temperatures and low rainfall. In these survey regions, 40 watermelon fields were selected, and 10 diseases were observed, including 4 fungal, 3 bacterial, 2 water mold, and 1 viral disease. The observed diseases were Anthracnose, Cercospora leaf spot, Fusarium wilt, Gummy stem blight, Downy mildew, Phytophthora fruit rot, Bacterial fruit blotch, Angular leaf spot, Yellow vine, and Watermelon mosaic disease. Molecular analysis was done in the Plant Pathology Lab at Sher-e-Bangla Agricultural University using the specific primers for fungal (ITS1/ITS4) and bacterial (27F/1492R) DNA regions and identified nine pathogen species, excluding the causal organism of the viral disease. The identified pathogens included Colletrotrichum orbiculare, Cercospora citrullina, Fusarium oxysporum, Stagonosporopsis cucurbitacearum, Pseudoperonospora cubensis, Phytophthora capsici, Acidovorax citrulli, Pseudomonas syringae, and Serratia marcescens. The sequencing of the identified pathogens revealed high homology (98.91–99.71%) with known sequences in the GenBank database. Phylogenetic analysis showed six clusters for fungal and water mold pathogen isolates and three for bacterial isolates where the percentages of replicate trees were 100% in all the cases. Among the identified diseases, the highest disease occurrence was caused by Fusarium wilt (47.5%) followed by Gummy stem blight (41.5%) in the Sylhet region and Angular leaf spot (37.5%) followed by Yellow vine (33%) in the Natore area. Fusarium wilt also has a high disease intensity, demonstrating its devastating impact on yield. This study highlights the influence of environmental conditions on disease incidence and underscores the need for tailored management strategies. These findings provide a foundation for developing targeted disease management practices for sustainable watermelon cultivation in Bangladesh. [ABSTRACT FROM AUTHOR]

The control of plant diseases represents a significant challenge in agriculture, particularly with the current emphasis on reducing pesticide use, necessitating alternative approaches. Among them, resistant plant breeding programs offer a promising alternative. Considering the stressful conditions in space, space conditions emerge as an innovative method for advancing crop improvement. This study explored the unique potential of the International Space Station (ISS) environment to induce beneficial modifications in grapevine, resulting in plants with reduced susceptibility to diseases. Canes of two Vitis vinifera L. cultivars, Cabernet Sauvignon (CS) and Merlot (Me), have undergone a 10-month space journey on-board the ISS, while others stayed on Earth (Ground Control, GC). We conducted a 2-year analysis of the response to downy mildew (Plasmopara viticola) of plants developed from ISS and GC canes, called Mother plants. The disease development of progenies produced from Merlot Mother plants was also evaluated. A higher proportion of individuals with low-susceptibility was noted in the ISS Mother group compared to the controls for both cultivars. This trend was also observed for the Merlot progenies. Finally, 11% of Merlot individuals (Mother and progenies, and for the 2 years of study) were distributed in the low susceptibility class. This study suggests that grapevine canes exposure to ISS conditions resulted in an enhanced percentage of plants showing reduction of susceptibility to downy mildew. [ABSTRACT FROM AUTHOR]

Although plant disease recognition has witnessed a significant improvement with deep learning in recent years, a common observation is that current deep learning methods with decent performance tend to suffer in real-world applications. We argue that this illusion essentially comes from the fact that current plant disease recognition datasets cater to deep learning methods and are far from real scenarios. Mitigating this illusion fundamentally requires an interdisciplinary perspective from both plant disease and deep learning, and a core question arises. What are the characteristics of a desired dataset? This paper aims to provide a perspective on this question. First, we present a taxonomy to describe potential plant disease datasets, which provides a bridge between the two research fields. We then give several directions for making future datasets, such as creating challenge-oriented datasets. We believe that our paper will contribute to creating datasets that can help achieve the ultimate objective of deploying deep learning in real-world plant disease recognition applications. To facilitate the community, our project is publicly available at https://github.com/xml94/PPDRD with the information of relevant public datasets. [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]

Introduction: There is a close and complex interaction between the elements in the aboveground-underground ecosystem during the growth and development of plants. Specifically, when the aboveground part of plants is infected by pathogens, it induces the plant rhizosphere to synthesize specific root exudates. Consequently, a group of beneficial rhizosphere soil bacteria is recruited to help plants resist diseases. However, the changes in the rhizosphere soil bacterial community of plants under infection by oomycete pathogens remain unknown. Methods: Three experimental treatments were set up in this experiment: soils inoculated with P. nicotianae , no-inoculation with P. nicotianae , and a control. The control treatment was composed of soils without transplanted tobacco plants, with the pathogen inoculated twice at an interval of eight days to ensure a successful P. nicotianae infection. P. nicotianae inoculation treatments were designed using the hyphal block inoculation method. In the non-inoculation treatment, tobacco plants were grown normally without pathogen inoculation. The tobacco plants were grown in a greenhouse. Results: This study demonstrates that tobacco plants recruit microorganisms at the rhizosphere level as a defense mechanism against disease after infection by the oomycete pathogen Phytophthora nicotianae. Specific rhizosphere soil bacteria were screened in vitro to promote tobacco growth in a biofilm-forming manner, which induced the systemic resistance of the plants to P. nicotianae. The recruitment of rhizosphere soil bacteria to the inter-root zone of tobacco plants after infection by P. nicotianae can help subsequently cultivated tobacco plants in the same soil resist pathogen infestation. Discussion: In conclusion, the present study confirms that infestation caused by oomycete pathogens alters the composition of the plant rhizosphere soil bacterial community and recruits a specific group of beneficial microorganisms that induce disease resistance and promote plant growth, thereby maximizing the protection of progeny grown in the same soil against the disease. [ABSTRACT FROM AUTHOR]

The early detection and accurate rate of classification of plant leaf disease are more important for reliable and good agriculture, which prevents unwanted financial loss and resources. In this study, Tangent Hunter Prey Optimization-based LeNet (THPO-LeNet) is utilized for crop leaf classification and multi-class plant leaf disease identification. In this case, the input image that goes through the image pre-processing step is obtained from the plant village dataset. An adaptive Wiener filter is applied at the pre-processing stage to reduce needless mistakes and improve image quality. The pre-processed image is then sent to the leaf segmentation step, where a Mask Region-based Convolution Neural Network (Mask R-CNN) performs the segmentation. Consequently, image augmentation is performed using techniques such as scaling, rotation, translation, flipping, contrast, saturation, and hue. Afterwards, first-level classification plant leaf classification is processed by LeNet, which is optimized by Tangent Hunter Prey Optimization (THPO). The THPO is the incorporation of a Tangent Search Algorithm (TSA) and Hunter–Prey Optimizer (HPO). At last, the second-level classification of plant leaf disease is conducted by THPO-LeNet. Furthermore, the efficiency of THPO-LeNet is examined based on measures, like accuracy, Negative Predictive Value (NPV), True Positive Rate (TPR), True Negative Rate (TNR), Positive Predictive Value (PPV), loss value, and False Positive Rate (FPR), and the value attained is 95.68%, 92.50%, 91.48%, 92.25%, 92.54%, 8.321%, and 7.754%, respectively. [ABSTRACT FROM AUTHOR]

Sweet potato (Ipomoea batatas) is a crucial crop for food security and economic stability in many regions, including Costa Rica. This study aimed to assess the prevalence and genetic diversity of two major viruses associated with sweet potato virus disease (SPVD) in Costa Rica: sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV). A total of 50 leaf samples displaying typical viral disease symptoms were collected from major sweet potato‐growing regions. Using multiplex reverse transcription (RT)‐PCR, SPFMV was detected in 82% of the samples and SPCSV in 52%, with a coinfection rate of 48%. Genetic analysis revealed that SPFMV isolates belonged predominantly to phylogenetic group B, while SPCSV isolates clustered with the West African (WA) strain. The low genetic diversity within these viral populations suggests a limited number of initial infection events followed by local spread. Riboprobe technology was evaluated as an alternative to RT‐PCR for virus detection. While the riboprobes for SPFMV demonstrated sensitivity comparable to RT‐PCR, the SPCSV riboprobes showed slightly lower sensitivity, particularly when using crude leaf extracts. Despite this, riboprobes offer significant advantages in terms of cost and ease of use for large‐scale screening. Our findings underscore the need for robust diagnostic and management strategies to control SPVD and highlight the importance of continuous monitoring and research to mitigate the impact of viral diseases on sweet potato production in Costa Rica. These insights contribute to the global understanding of SPVD and support collaborative efforts in plant pathology research. [ABSTRACT FROM AUTHOR]

This study focuses on identifying and evaluating the severity of powdery mildew disease in tomato plants. The uniqueness of this work lies in combining the imaging and advanced deep learning methods to develop a technique that transforms Red Green Blue (RGB) images into Simulated Hyperspectral Images (SHSI) to perform spectral and spatial analysis for precise detection and assessment of powdery mildew severity, thereby enhancing disease management. Furthermore, this research evaluates three advanced pre-trained VGG16 models, ResNet50 and EfficientNet-B7 algorithms for image preprocessing and feature extraction. Extracted features are passed to a neural network generator model to convert RGB image features into SHSIs, providing insights into the spectrum. This method enables the image analysis to perform assessments from SHSIs for health classification using Normalized Difference Vegetation Index (NDVI) values, which are meticulously compared with accurate hyperspectral data using metrics like mean absolute error (MAE) and root mean squared error (RMSE). This strategy enhances precision farming, environmental monitoring, and remote sensing accuracy. Results show that ResNet50's architecture offers a robust framework for this study's spectral and spatial analysis, making it a suitable choice over VGG16 and EfficientNet-B7 for transforming RGB images into SHSI. These simulated hyperspectral images offer a scalable and affordable approach for precise assessment of crop disease severity. [ABSTRACT FROM AUTHOR]

Introduction: Long-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence. Methods: This study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation. Results and discussion: Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus , Rubrobacter , Luteitalea , Nakamurella , and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community. [ABSTRACT FROM AUTHOR]

Introduction: Zanthoxylum bungeanum Maxim is an economically significant crop in Asia, but large-scale cultivation is often threatened by frequent diseases, leading to significant yield declines. Deep learning-based methods for crop disease recognition have emerged as a vital research area in agriculture. Methods: This paper presents a novel model, LT-DeepLab, for the semantic segmentation of leaf spot (folium macula), rust, frost damage (gelu damnum), and diseased leaves and trunks in complex field environments. The proposed model enhances DeepLabV3+ with an innovative Fission Depth Separable with CRCC Atrous Spatial Pyramid Pooling module, which reduces the structural parameters of Atrous Spatial Pyramid Pooling module and improves cross-scale extraction capability. Incorporating Criss-Cross Attention with the Convolutional Block Attention Module provides a complementary boost to channel feature extraction. Additionally, deformable convolution enhances low-dimensional features, and a Fully Convolutional Network auxiliary header is integrated to optimize the network and enhance model accuracy without increasing parameter count. Results: LT-DeepLab improves the mean Intersection over Union (mIoU) by 3.59%, the mean Pixel Accuracy (mPA) by 2.16%, and the Overall Accuracy (OA) by 0.94% compared to the baseline DeepLabV3+. It also reduces computational demands by 11.11% and decreases the parameter count by 16.82%. Discussion: These results indicate that LT-DeepLab demonstrates excellent disease segmentation capabilities in complex field environments while maintaining high computational efficiency, offering a promising solution for improving crop disease management efficiency. [ABSTRACT FROM AUTHOR]

Trichoderma species are ubiquitous saprophytic fungi commonly found in soil, with potential as fungal biocontrol agents for plant disease control and growth promotion. This research aimed to assess the attributes of Trichoderma sp. as plant growth promoters, focusing on nitrogen fixation, siderophore production, plant nutrient solubilization and indole-3-acetic acid production. Out of 19 isolates tested, 6 (T05, T19, T25, T27, T28 and T33) showed superior plant growth promotion abilities. These isolates were further evaluated for their capacity to enhance the germination of Khao Dawk Mali 105 rice seeds. Seeds were soaked in a suspension of conidia at a concentration of 1x1012 conidia/mL, and germination rates were measured. The germination rate ranged between 77.67 - 86.67%, statistically significantly higher than the control rate of 33.33%. Among the isolates, T05 exhibited the highest promotion of plant growth, evidenced by root length (7.27 cm), shoot length (8.50 cm), fresh weight (0.54 g) and dry weight (0.27 g), all significantly different from the control. Additionally, the potential of isolates to inhibit the fungal pathogen Colletotrichum sp. MN-3 was assessed using a dual culture method, with T35 showing the highest inhibition percentage (60.90%). Morphological classification and nucleotide sequencing of the ITS1-5.8S-ITS2 region of rDNA gene identified the isolates as T. harzianum, T. reesei, T. asperellum and T. longibrachiatum. These findings underscore the effectiveness of Trichoderma sp. in promoting plant growth and suppressing plant pathogenic fungi. [ABSTRACT FROM AUTHOR]

Transcriptomes from stem-inoculated Scots pine saplings were analyzed to identify unique and enriched H. annosum transcripts in the early stages of infection. Comparing different time points since inoculation identified 131 differentially expressed H. annosum genes with p-values of ≤0.01. Our research supports the results of previous studies on the Norway spruce–Heterobasidion annosum s.l. pathosystem, indicating the role of carbohydrate and lignin degradation genes in pathogenesis at different time points post-inoculation and the role of lipid metabolism genes (including but not limited to the delta-12 fatty acid desaturase gene previously reported to be an important factor). The results of this study indicate that the malic enzyme could be a potential gene of interest in the context of H. annosum virulence. During this study, difficulties related to incomplete reference material of the host plant species and a low proportion of H. annosum transcripts in the RNA pool were encountered. In addition, H. annosum transcripts are currently not well annotated. Improvements in sequencing technologies (including sequencing depth) or bioinformatics focusing on small subpopulations of RNA would be welcome. [ABSTRACT FROM AUTHOR]

Plant growth‐promoting rhizobacteria (e.g., Bacillus) confer health benefits to the host. Bacillus siamensis has been used to control plant disease in fruits and vegetables, but its potential effects on crop performance remain unclear. This study investigated changes in the growth, root transcriptomic profile, and rhizosp here microbiome of maize plants (Zea may L.) following inoculation with B. siamensis 33. All inoculated plants grew better than non‐inoculated controls in pots, as exemplified by 24.0% and 6.8% increase in plant height and stem diameter, respectively (p < 0.01). Shoot dry weight also increased by 20.6% upon inoculation, accompanied by 46.9% increase in root dry weight (p < 0.01). Transcriptomic analysis revealed that inoculation induced (2.16‐ to 5.53‐fold) upregulated expression of genes related to auxin signal transduction in maize. The expression of genes involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant defense‐related signal (e.g., jasmonic acid and salicylic acid) transduction was (2.06‐ to 11.30‐fold) upregulated in inoculated plants. Upon inoculation, bacterial α‐diversity trended higher and potentially beneficial taxa (e.g., Sphingobium, Flavihumibacter, and Parasegetibacter) were enriched in the rhizosphere, likely a result of enhanced root exudation of specific metabolites (e.g., flavonoids) and subsequent recruitment of beneficial microbial taxa. Potential microbial functions associated with nitrogen cycling and pollutant degradation were stimulated by inoculation. These findings indicate that B. siamensis 33 mediates the reprogramming of plant gene expression and reshaping of rhizosphere microbiome structure to bolster maize crop performance. Core Ideas: We uncovered the changes in maize plants and rhizosphere microbiomes after inoculation with Bacillus siamensis.Bacillus siamensis mediated the reprogramming of plant gene expression in roots.Potentially beneficial bacteria were enriched in the rhizosphere of inoculated plants.Inoculation stimulated rhizosphere bacterial community complexity and potential functions.Bacillus siamensis mediates plant gene reprogramming and rhizosphere microbiome reshaping to enhance crop performance. [ABSTRACT FROM AUTHOR]

Agriculture is the strength of our nation, and its production rate is also important for feeding food to all. The crop production rate is more significantly affected by various diseases. Currently, these diseases are identified and classified using a visual inspection method, which is not suitable for larger crop fields. Therefore, a machine-based, systematic approach is needed to identify various diseases that occur on the leaves of the jasmine plant. The present article develops and proposes a computer-based systematic approach to the detection and diagnosis of jasmine plant diseases using the dual deep learning method. The proposed classifier consists of a general adversarial network (GAN) module and a proposed convolutional neural network (CNN) architecture for diagnosing diseases in the jasmine plant. The GAN module extracts the features from the dataaugmented jasmine plant leaf image, and the CNN module performs the disease classification process. The proposed CNN module contains both lower and higherorder kernels that produce the hybrid features, which are further classified by the CNN architecture. The proposed classification approach is validated on the set of jasmine plant leaf images. The simulation is carried out using MATLAB software, and the results of the plant leaf classification system are compared with state-of-the-art models in terms of crop sensitivity, crop specificity and accuracy. [ABSTRACT FROM AUTHOR]

• Fungal metabolites and nanoparticles suppress disease severity. • Fungal metabolites and nanoparticles reduced oxidative stress in tomato plants. • These treatments positively regulate microbial communities in the soil. • Microbial communities showed more abundance by the application of fungal metabolites and nanoparticles. Numerous techniques have been adopted to promote crop growth and improve the effectiveness of biological control. One of these strategies includes the utilization of antimicrobial metabolites from biocontrol agents combined with other strategies. Nanotechnology is a novel and emerging trend in controlling plant diseases. The present study aimed to improve the understanding through an assessment of the mechanism of how the co-application of nanoparticles (SiNPS) and fungal metabolites prevent tomato bacterial wilt infection and explore how the applied treatments regulate the soil microbial community structures present in the rhizosphere of tomato plants. It was demonstrated under in-vitro conditions that the silicon nanoparticles and metabolites of fungi restricted the growth of Ralstonia solanacearum , the causal agent of bacterial wilt. The combined application of nanoparticles and fungal metabolites during planta investigation significantly reduced the disease severity and improved plant growth. These treatments caused significant changes in rhizosphere microbial communities and enhanced the abundance of plant-beneficial microbes. The results of the current study hence advocate the application of fungal metabolites and SiNPS as an effective and environment-friendly strategy for controlling the wilt disease of bacteria in tomato plants and various other host crops. [ABSTRACT FROM AUTHOR]

Sickle cell disease (SCD) is one of the most devastating inherited haemoglobinopathy that affects mostly children. Its prevalence can reach up to 13 % in the south-eastern part of Madagascar. For socio-cultural and economic reasons, the majority of patients use plants to manage the symptoms of this genetic disease. This work aims to inventory these plants and collect all information on their use, their therapeutic effects, and their eventual side effects in order to compile a database. These plants will be the subject of future chemical, pharmacological and toxicological investigations in the laboratory. Semi-directive interviews were led among 208 respondents from January 2018 to January 2020 in the eastern part of Madagascar. After obtaining the informed consent of the interviewees, collected data on the used medicinal plants were analyzed for various ethnomedicinal parameters including frequency of citation (FC), use value (UV), relative frequency of citation (RFC), fidelity level (FL), family use value (FUV) and informant consensus factor (ICF) related to the SCD management and the other mentioned diseases. Among the 208 respondents, 30.29 % were male; 73.39 % received formal education; 53.37 % were farmers, 8.17 % were traditional healers and 6.73 % were herbal sellers. Most of them (94.23 %) have a good knowledge of SCD and 91.83 % of them use herbal medicine to manage SCD. They recommended 123 plant species belonging to 111 genera and 62 families. Asteraceae (14.50 %) was the most cited family however Blechnaceae was the most valued family (FUV = 0.356). The majority of the cited species (70.73 %) were wild plants. Herbs (42.28 %) were the most used plant life form and the most used common parts were leaves (44.68 %). They usually prepare tea by infusion of plant material (71.83 %). Ficus polita was the most important species with the highest FC (10.93 %), UV (0.393), RFC (75.92 %) and FL (94.94 %). ICF of SCD and its symptoms value was 0.50 showing the homogeneity, and the consensus among the informants in the use of medicinal plants for managing this disease. Some species (08) have been reported for their anti-sickling properties and some of the other species have been reported for their pharmacological properties related to SCD symptoms management. These results confirmed the importance of investigating the use of plant species to manage SCD and its symptoms in the eastern part of Madagascar, suggesting the fundamental role of ethnomedicinal studies for the sustainable use of plant species for future scientific investigations on phyto-drugs for SCD management. [Display omitted] • 123 plant species were cited in the management of SCD and/or its symptoms. • The majority (70.73 %) of them were wild plants. • Herbs (42.28 %) was the most used plant life form and the most used common parts were leaves (44.68 %) and aerial parts (25.53 %). • The majority of the herbal preparation was infusion (71.83 %) and the administration is only by oral route. • The knowledge of medicinal plants depends on the age and the occupation of the informants. • Ficus polita and Stenochlaena tenuifolia were the most important species according to their use value. • Among the 123 species, 8 species have been reported for their anti-sickling properties. [ABSTRACT FROM AUTHOR]