The persistent threat of emerging plant disease pandemics to global food security

Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight

Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.

Revolutionizing agriculture with nanotechnology: Innovative approaches in fungal disease management and plant health monitoring

Nanotechnology has emerged as a transformative force in modern agriculture, offering innovative solutions to address challenges related to fungal plant diseases and overall agricultural productivity. Specifically, the antifungal activities of metal, metal oxide, bio-nanoparticles, and polymer nanoparticles were examined, highlighting their unique mechanisms of action against fungal pathogens. Nanoparticles can be used as carriers for fungicides, offering advantages in controlled release, targeted delivery, and reduced environmental toxicity. Nano-pesticides and nano-fertilizers can enhance nutrient uptake, plant health, and disease resistance were explored. The development of nanosensors, especially those utilizing quantum dots and plasmonic nanoparticles, promises early and accurate detection of fungal pathogens, a crucial step in timely disease management. However, concerns about their potential toxic effects on non-target organisms, environmental impacts, and regulatory hurdles underscore the importance of rigorous research and impact assessments. The review concludes by emphasizing the significant prospects of nanotechnology in reshaping the future of agriculture but advocates for a balanced approach that prioritizes safety, sustainability, and environmental stewardship.

Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters

Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Selenium Nanomaterials Enhance Sheath Blight Resistance and Nutritional Quality of Rice: Mechanisms of Action and Human Health Benefit

In the current work, the foliar application of selenium nanomaterials (Se0 NMs) suppressed sheath blight in rice (Oryza sativa). The beneficial effects were nanoscale specific and concentration dependent. Specifically, foliar amendment of 5 mg/L Se0 NMs decreased the disease severity by 68.8% in Rhizoctonia solani-infected rice; this level of control was 1.57- and 2.20-fold greater than that of the Se ions with equivalent Se mass and a commercially available pesticide (Thifluzamide). Mechanistically, (1) the controlled release ability of Se0 NMs enabled a wider safe concentration range and greater bioavailability to Se0 NMs, and (2) transcriptomic and metabolomic analyses demonstrated that Se0 NMs simultaneously promoted the salicylic acid- and jasmonic-acid-dependent acquired disease resistance pathways, antioxidative system, and flavonoid biosynthesis. Additionally, Se0 NMs improved rice yield by 31.1%, increased the nutritional quality by 6.4-7.2%, enhanced organic Se content by 44.8%, and decreased arsenic and cadmium contents by 38.7 and 42.1%, respectively, in grains as compared with infected controls. Human simulated gastrointestinal tract model results showed that the application of Se0 NMs enhanced the bioaccessibility of Se in grains by 22.0% and decreased the bioaccessibility of As and Cd in grains by 20.3 and 13.4%, respectively. These findings demonstrate that Se0 NMs can serve as an effective and sustainable strategy to increase food quality and security.

From Pipeline to Plant Protection Products: Using New Approach Methodologies (NAMs) in Agrochemical Safety Assessment

The human population will be approximately 9.7 billion by 2050, and food security has been identified as one of the key issues facing the global population. Agrochemicals are an important tool available to farmers that enable high crop yields and continued access to healthy foods, but the average new agrochemical active ingredient takes more than ten years, 350 million dollars, and 20,000 animals to develop and register. The time, monetary, and animal costs incentivize the use of New Approach Methodologies (NAMs) in early-stage screening to prioritize chemical candidates. This review outlines NAMs that are currently available or can be adapted for use in early-stage screening agrochemical programs. It covers new in vitro screens that are on the horizon in key areas of regulatory concern. Overall, early-stage screening with NAMs enables the prioritization of development for agrochemicals without human and environmental health concerns through a more directed, agile, and iterative development program before animal-based regulatory testing is even considered.

Integrative transcriptomic and metabolomic analyses reveals the toxicity and mechanistic insights of bioformulated chitosan nanoparticles against Magnaporthe oryzae

Rice blast, an extremely destructive disease caused by the filamentous fungal pathogen Magnaporthe oryzae, poses a global threat to the production of rice (Oryza sativa L.). The emerging trend of reducing dependence on chemical fungicides for crop protection has increased interest in exploring bioformulated nanomaterials as a sustainable alternative antimicrobial strategy for effectively managing plant diseases. Herein, we used physiomorphological, transcriptomic, and metabolomic methods to investigate the toxicity and molecular action mechanisms of moringa-chitosan nanoparticles (M-CNPs) against M. oryzae. Our results demonstrate that M-CNPs exhibit direct antifungal properties by impeding the growth and conidia formation of M. oryzae in a concentration-dependent manner. Propidium iodide staining indicated concentration-dependent significant apoptosis (91.33%) in the fungus. Ultrastructural observations revealed complete structural damage in fungal cells treated with 200 mg/L M-CNPs, including disruption of the cell wall and destruction of internal organelles. Transcriptomic and metabolomic analyses revealed the intricate mechanism underlying the toxicity of M-CNPs against M. oryzae. The transcriptomics data indicated that exposure to M-CNPs disrupted various processes integral to cell membrane biosynthesis, aflatoxin biosynthesis, transcriptional regulation, and nuclear integrity in M. oryzae., emphasizing the interaction between M-CNPs and fungal cells. Similarly, metabolomic profiling demonstrated that exposure to M-CNPs significantly altered the levels of several key metabolites involved in the integral components of metabolic pathways, microbial metabolism, histidine metabolism, citrate cycle, and lipid and protein metabolism in M. oryzae. Overall, these findings demonstrated the potent antifungal action of M-CNPs, with a remarkable impact at the physiological and molecular level, culminating in substantial apoptotic-like fungal cell death. This research provides a novel perspective on investigating bioformulated nanomaterials as antifungal agents for plant disease control.

Understanding the Effects of Ligand Configuration on Protoporphyrinogen IX Oxidase with Rationally Designed 3-(N-Phenyluracil)but-2-enoates

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) is a promising target for green herbicide discovery. However, the ligand configuration effects on PPO activity were still poorly understood. Herein, we designed 3-(N-phenyluracil)but-2-enoates using our previously developed active fragments exchange and link (AFEL) approach and synthesized a series of novel compounds with nanomolar ranges of Nicotiana tabacum PPO (NtPPO) inhibitory potency and promising herbicidal potency. Our systematic structure-activity relationship investigations showed that the E isomers of 3-(N-phenyluracil)but-2-enoates displayed improved bioactivity than their corresponding Z isomers. Using molecular simulation studies, we found that the E isomers showed a relatively lower entropy change and could sample more stable binding conformation to the receptor than the Z isomers. Our density functional theory (DFT) calculations showed that the E isomers showed higher chemical reactivity and lower electronic chemical potential than their corresponding Z isomers. Compound E-Ic emerged as the optimal compound with a Ki value of 3.0 nM against NtPPO, exhibiting a broader spectrum of weed control than saflufenacil at 37.5-75 g ai/ha and also safe to maize at 75 g ai/ha, which could be considered as a promising lead herbicide for further development.

Viral Threats to Fruit and Vegetable Crops in the Caribbean

Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.

Beyond the β-amino alcohols framework: identification of novel β-hydroxy pyridinium salt-decorated pterostilbene derivatives as bacterial virulence factor inhibitors

BACKGROUND

Bacterial virulence factors are involved in various biological processes and mediate persistent bacterial infections. Focusing on virulence factors of phytopathogenic bacteria is an attractive strategy and crucial direction in pesticide discovery to prevent invasive and persistent bacterial infection. Hence, discovery and development of novel agrochemicals with high activity, low-risk, and potent anti-virulence is urgently needed to control plant bacterial diseases.

RESULTS

A series of novel β-hydroxy pyridinium cation decorated pterostilbene derivatives were prepared and their antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo) were systematacially assessed. Among these pterostilbene derivatives, compound 4S exhibited the best antibacterial activity against Xoo in vitro, with an half maximal effective concentration (EC50) value of 0.28 μg mL-1. A series of biochemical assays including scanning electron microscopy, crystal violet staining, and analysis of biofilm formation, swimming motility, and related virulence factor gene expression levels demonstrated that compound 4S could function as a new anti-virulence factor inhibitor by interfering with the bacterial infection process. Furthermore, the pot experiments provided convinced evidence that compound 4S had the high control efficacy (curative activity: 71.4%, protective activity: 72.6%), and could be used to effectively manage rice bacterial leaf blight in vivo.

CONCLUSION

Compounds 4S is an attractive virulence factor inhibitor with potential for application in treating plant bacterial diseases by suppressing production of several virulence factors. © 2024 Society of Chemical Industry.

Pooled effector library screening in protoplasts rapidly identifies novel Avr genes

Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) after screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution via genotype surveillance, which in turn will lead to optimized R gene stacking and deployment strategies. This platform should be broadly applicable to many crop pathogens and could potentially be adapted for screening genes involved in other protoplast-selectable traits.

Phenological evolution in annual plants under light competition, changes in the growth season and mass loss

Flowering time is an important phenological trait in plants and a critical determinant of the success of pollination and fruit or seed development, with immense significance for agriculture as it directly affects crop yield and overall food production. Shifts in the growth season, changes in the growth season duration and changes in the production rate are environmental processes (potentially linked to climate change) that can lead to changes in flowering time in the long-term due to selection. In contrast, biomass loss (due to, for example, herbivory or diseases) can have profound consequences for plant mass production and food security. We model the effects of these environmental processes on the flowering time evolutionarily stable strategy (ESS) of annual plants and the potential consequences for reproductive output. Our model recapitulates previous theoretical results linked to climate change and light competition and makes novel predictions about the effects of biomass loss on the evolution of flowering time. Our analysis elucidates how both the magnitude and direction of the evolutionary response can depend on whether biomass loss occurs during the earlier vegetative phase or during the later reproductive phase and on whether or not plants are adapted to grow in dense, competitive environments. Specifically, light competition generates an asymetric effect of mass loss on flowering time even when loss is indiscriminate (equal rates), with vegetative mass loss having a stronger effect on flowering time (resulting in greater ESS change) and final reproductive output.

A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions

Plants intricately deploy defense systems to counter diverse biotic and abiotic stresses. Omics technologies, spanning genomics, transcriptomics, proteomics, and metabolomics, have revolutionized the exploration of plant defense mechanisms, unraveling molecular intricacies in response to various stressors. However, the complexity and scale of omics data necessitate sophisticated analytical tools for meaningful insights. This review delves into the application of artificial intelligence algorithms, particularly machine learning and deep learning, as promising approaches for deciphering complex omics data in plant defense research. The overview encompasses key omics techniques and addresses the challenges and limitations inherent in current AI-assisted omics approaches. Moreover, it contemplates potential future directions in this dynamic field. In summary, AI-assisted omics techniques present a robust toolkit, enabling a profound understanding of the molecular foundations of plant defense and paving the way for more effective crop protection strategies amidst climate change and emerging diseases.

Photosynthesis of rice leaves with a parallel venation is highly tolerant to vein severing

Vein severing in plants caused by leaf damage is common in fields where crops are cultivated. It is hypothesized that leaves with complex reticulate venation can withstand hydraulic disturbances caused by vein severing, thereby preserving leaf carbon assimilation. However, limited research focuses on vein damage of leaves with parallel venation. We studied how vein-severing affected the photosynthetic traits of rice (Oryza sativa) leaves in seconds, minutes and days, under varying water-demand conditions and differing extents of water supply disruption. Rice leaves completely lost their photosynthetic capacity within 2.5 minutes after excision. Severing the midrib resulted in reduced light-saturated photosynthetic rate (A), stomatal conductance (gsw ) and transpiration rate (E) by 2.6, 6.8 and 5.9%, respectively, already after thirty minutes. We further investigated the photosynthetic trait responses to various extents of leaf width severing, while keeping the midrib functional. Surprisingly, A, gsw and E in the downstream area of the severed leaves largely remained stable, showing minimal variation across different leaf width severing ratios. These traits declined only slightly even under increased ambient light intensity and leaf-to-air vapor pressure deficit. This sustained photosynthesis post-severing is attributed to the efficient lateral water transport. Long-term leaf damage slightly but not significantly, impacted the downstream photosynthetic traits within five days post-severing. However, a more pronounced reduction in gas exchange during leaf senescence was observed nine days after severing. These findings suggested that rice leaves can tolerate hydraulic disturbances from vein severing and maintain functionality under various conditions, which is crucial for crop yield stability. However, long-term consequences require further investigation.

Cost-optimal seeding strategy during a botanical pandemic in domesticated fields

Botanical pandemics cause enormous economic damage and food shortages around the globe. However, since botanical pandemics are here to stay in the short-medium term, domesticated field owners can strategically seed their fields to optimize each session's economic profit. In this work, we propose a novel epidemiological-economic mathematical model that describes the economic profit from a field of plants during a botanical pandemic. We describe the epidemiological dynamics using a spatiotemporal extended susceptible-infected-recovered epidemiological model with a non-linear output economic model. We provide an algorithm to obtain an optimal grid-formed seeding strategy to maximize economic profit, given field and pathogen properties. We show that the recovery and basic infection rates have a similar economic influence. Unintuitively, we show that a larger farm does not promise higher economic profit. Our results demonstrate a significant benefit of using the proposed seeding strategy and shed more light on the dynamics of the botanical pandemic.

A review on endophytic fungi: a potent reservoir of bioactive metabolites with special emphasis on blight disease management

Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.

Reconstructing historic and modern potato late blight outbreaks using text analytics

In 1843, a hitherto unknown plant pathogen entered the US and spread to potato fields in the northeast. By 1845, the pathogen had reached Ireland leading to devastating famine. Questions arose immediately about the source of the outbreaks and how the disease should be managed. The pathogen, now known as Phytophthora infestans, still continues to threaten food security globally. A wealth of untapped knowledge exists in both archival and modern documents, but is not readily available because the details are hidden in descriptive text. In this work, we (1) used text analytics of unstructured historical reports (1843-1845) to map US late blight outbreaks; (2) characterized theories on the source of the pathogen and remedies for control; and (3) created modern late blight intensity maps using Twitter feeds. The disease spread from 5 to 17 states and provinces in the US and Canada between 1843 and 1845. Crop losses, Andean sources of the pathogen, possible causes and potential treatments were discussed. Modern disease discussion on Twitter included near-global coverage and local disease observations. Topic modeling revealed general disease information, published research, and outbreak locations. The tools described will help researchers explore and map unstructured text to track and visualize pandemics.

Discovery, Identification, and Mode of Action of Phenolics from Marine-Derived Fungus Aspergillus ustus as Antibacterial Wilt Agents

The bacterial wilt caused by Ralstonia solanacearum seriously affects crop yield and safety and is difficult to control. Biological activity-guided screening led to the isolation of 11 phenolic compounds including three undescribed compounds (carnemycin H-I and stromemycin B) from the secondary metabolites of a marine-derived Aspergillus ustus. One new compound is an unusual phenolic dimer. Their structures were elucidated by comprehensive spectroscopic data and J-based configurational analysis. The antibacterial activities of the isolated compounds against R. solanacearum were evaluated. Compound 3 exhibited excellent inhibitory activity with an MIC value of 3 μg/mL, which was comparable to that of streptomycin sulfate. Additionally, 3 significantly changed the morphology and inhibited the activity of succinate dehydrogenase (SDH) to interfere with the growth of R. solanacearum. Molecular docking was conducted to clarify the potential mechanisms of compound 3 with SDH. Further in vivo experiments demonstrated that 3 could remarkably inhibit the occurrence of bacterial wilt on tomatoes.

Coherent spore dispersion via drop-leaf interaction

The dispersion of plant pathogens, such as rust spores, is responsible for more than 20% of global crop yield loss annually. However, the release mechanism of pathogens from flexible plant surfaces into the canopy is not well understood. In this study, we investigated the interplay between leaf elasticity and rainfall, revealing how a flexible leaf structure can generate a lateral flow stream, with embedded coherent structures that enhance transport. We first modeled the linear coupling between drop momentum, leaf vibration, and the stream flux from leaf surfaces. With Lagrangian diagnostics, we further mapped out the nested coherent structures around the fluttering profile, providing a dynamical description for local spore delivery. We hope the mechanistic details extracted here can facilitate the construction of physically informed analytical models for local crop disease management.

Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole-genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini-chromosome. Genome assembly of a Zambian strain revealed that its mini-chromosome was similar to the B71 mini-chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini-chromosomes have undergone marked diversification. The maintenance of the mini-chromosome and rapid genomic changes suggest the mini-chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.

Preparation and assessment of alginate-microencapsulated Trichoderma harzianum for controlling Sclerotinia sclerotiorum and Rhizoctonia solani on tomato

This study aimed to develop microencapsulation technology using alginate to improve the viability and performance of Trichoderma harzianum. The method of ionic gelation was used to prepare the microparticles, and the efficiency of encapsulation was estimated to be 99%. The average size of the prepared microspheres was 2600 μm (wet) and 1000 μm (dry). Scanning electron microscopy revealed that the microspheres were approximately spherical. Fourier transform infrared spectrophotometer analysis indicated an interaction between T. harzianum and the microspheres. The results of temperature resistance and light stability against ultraviolet radiation emphasized the positive impact of microencapsulation in improving the viability and resistance of T. harzianum compared to the non-microencapsulated state. The disease percentage of Rhizoctonia solani and Sclerotinia sclerotiorum in plants treated with microencapsulated T. harzianum microcapsules was 8.88 % and 20 % respectively, but in the control group was 73.33 % (p ≤ 0.05).

Recent advances in immuno-based methods for the detection of Ralstonia solanacearum

Ralstonia solanacearum (RS) is a widely recognized phytopathogenic bacterium which is responsible for causing devastating losses in a wide range of economically significant crops. Timely and accurate detection of this pathogen is pivotal to implementing effective disease management strategies and preventing crop losses. This review provides a comprehensive overview of recent advances in immuno-based detection methods for RS. The review begins by introducing RS, highlighting its destructive potential and the need for point-of-care detection techniques. Subsequently, it explores traditional detection methods and their limitations, emphasizing the need for innovative approaches. The main focus of this review is on immuno-based detection methods and it discusses recent advancements in serological detection techniques. Furthermore, the review sheds light on the challenges and prospects of immuno-based detection of RS. It emphasizes the importance of developing rapid, field-deployable assays that can be used by farmers and researchers alike. In conclusion, this review provides valuable insights into the recent advances in immuno-based detection methods for RS.

Transgressive segregation, hopeful monsters, and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance to Macrophomina in strawberry

Two decades have passed since the strawberry (Fragaria x ananassa) disease caused by Macrophomina phaseolina, a necrotrophic soilborne fungal pathogen, began surfacing in California, Florida, and elsewhere. This disease has since become one of the most common causes of plant death and yield losses in strawberry. The Macrophomina problem emerged and expanded in the wake of the global phase-out of soil fumigation with methyl bromide and appears to have been aggravated by an increase in climate change-associated abiotic stresses. Here we show that sources of resistance to this pathogen are rare in gene banks and that the favorable alleles they carry are phenotypically unobvious. The latter were exposed by transgressive segregation and selection in populations phenotyped for resistance to Macrophomina under heat and drought stress. The genetic gains were immediate and dramatic. The frequency of highly resistant individuals increased from 1% in selection cycle 0 to 74% in selection cycle 2. Using GWAS and survival analysis, we found that phenotypic selection had increased the frequencies of favorable alleles among 10 loci associated with resistance and that favorable alleles had to be accumulated among four or more of these loci for an individual to acquire resistance. An unexpectedly straightforward solution to the Macrophomina disease resistance breeding problem emerged from our studies, which showed that highly resistant cultivars can be developed by genomic selection per se or marker-assisted stacking of favorable alleles among a comparatively small number of large-effect loci.

Label-Free Surface-Enhanced Raman Scattering Detection of Fire Blight Pathogen Using a Pathogen-Specific Bacteriophage

Fire blight is one of the most devastating plant diseases, causing severe social and economic problems. Herein, we report a novel method based on label-free surface-enhanced Raman scattering (SERS) combined with an Erwinia amylovora-specific bacteriophage that allows detecting efficiently fire blight bacteria E. amylovora for the first time. To achieve the highest SERS signals for E. amylovora, we synthesized and compared plasmonic nanoparticles (PNPs) with different sizes, i.e., bimetallic gold core-silver shell nanoparticles (Au@AgNPs) and monometallic gold nanoparticles (AuNPs) and utilized the coffee-ring effect for the self-assembly of PNPs and enrichment of fire blight bacteria. Furthermore, we investigated the changes in the SERS spectra of E. amylovora after incubation with an E. amylovora-specific bacteriophage, and we found considerable differences in the SERS signals as a function of the bacteriophage incubation time. The results indicate that our bacteriophage-based label-free SERS analysis can specifically detect E. amylovora without the need for peak assignment on the SERS spectra but simply by monitoring the changes in the SERS signals over time. Therefore, our facile method holds great potential for the label-free detection of pathogenic bacteria and the investigation of viral-bacterial interactions.

Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae

Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.

Bioinspired silver nanoparticle-based nanocomposites for effective control of plant pathogens: A review

Plant pathogens, including bacteria, fungi, and viruses, pose significant challenges to the farming community due to their extensive diversity, the rapidly evolving phenomenon of multi-drug resistance (MDR), and the limited availability of effective control measures. Amid mounting global pressure, particularly from the World Health Organization, to limit the use of antibiotics in agriculture and livestock management, there is increasing consideration of engineered nanomaterials (ENMs) as promising alternatives for antimicrobial applications. Studies focusing on the application of ENMs in the fight against MDR pathogens are receiving increasing attention, driven by significant losses in agriculture and critical knowledge gaps in this crucial field. In this review, we explore the potential contributions of silver nanoparticles (AgNPs) and their nanocomposites in combating plant diseases, within the emerging interdisciplinary arena of nano-phytopathology. AgNPs and their nanocomposites are increasingly acknowledged as promising countermeasures against plant pathogens, owing to their unique physicochemical characteristics and inherent antimicrobial properties. This review explores recent advancements in engineered nanocomposites, highlights their diverse mechanisms for pathogen control, and draws attention to their potential in antibacterial, antifungal, and antiviral applications. In the discussion, we briefly address three crucial dimensions of combating plant pathogens: green synthesis approaches, toxicity-environmental concerns, and factors influencing antimicrobial efficacy. Finally, we outline recent advancements, existing challenges, and prospects in scholarly research to facilitate the integration of nanotechnology across interdisciplinary fields for more effective treatment and prevention of plant diseases.

Scientific and technological advances in the development of sustainable disease management tools: a case study on kiwifruit bacterial canker

Plant disease outbreaks are increasing in a world facing climate change and globalized markets, representing a serious threat to food security. Kiwifruit Bacterial Canker (KBC), caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), was selected as a case study for being an example of a pandemic disease that severely impacted crop production, leading to huge economic losses, and for the effort that has been made to control this disease. This review provides an in-depth and critical analysis on the scientific progress made for developing alternative tools for sustainable KBC management. Their status in terms of technological maturity is discussed and a set of opportunities and threats are also presented. The gradual replacement of susceptible kiwifruit cultivars, with more tolerant ones, significantly reduced KBC incidence and was a major milestone for Psa containment - which highlights the importance of plant breeding. Nonetheless, this is a very laborious process. Moreover, the potential threat of Psa evolving to more virulent biovars, or resistant lineages to existing control methods, strengthens the need of keep on exploring effective and more environmentally friendly tools for KBC management. Currently, plant elicitors and beneficial fungi and bacteria are already being used in the field with some degree of success. Precision agriculture technologies, for improving early disease detection and preventing pathogen dispersal, are also being developed and optimized. These include hyperspectral technologies and forecast models for Psa risk assessment, with the latter being slightly more advanced in terms of technological maturity. Additionally, plant protection products based on innovative formulations with molecules with antibacterial activity against Psa (e.g., essential oils, phages and antimicrobial peptides) have been validated primarily in laboratory trials and with few compounds already reaching field application. The lessons learned with this pandemic disease, and the acquired scientific and technological knowledge, can be of importance for sustainably managing other plant diseases and handling future pandemic outbreaks.

Zero-exemplar deep continual learning for crop disease recognition: a study of total variation attention regularization in vision transformers

With the increasing integration of AI technology in the food industry, deep learning has demonstrated its immense potential in the domain of plant disease image recognition. However, there remains a gap in research between models capable of continual learning of new diseases and addressing the inherent catastrophic forgetting issue in neural networks. This study aims to comprehensively evaluate various learning strategies based on advanced computer vision models for multi-disease continual learning tasks in food disease recognition. To cater to the benchmark dataset requirements, we collected the PlantDiseaseCL dataset, sourced from the internet, encompassing diverse crop diseases from apples, corn, and more. Utilizing the Vision Transformer (ViT) model, we established a plant disease image recognition classifier, which, in joint learning, outperformed several comparative CNN architectures in accuracy (0.9538), precision (0.9532), recall (0.9528), and F1 score (0.9560). To further harness the potential of ViT in food disease defect recognition, we introduced a mathematical paradigm for crop disease recognition continual learning. For the first time, we proposed a novel ViT-TV architecture in the multi-disease image recognition scenario, incorporating a Total Variation (TV) distance-based loss (TV-Loss) to quantify the disparity between current and previous attention distributions, fostering attention consistency and mitigating the catastrophic forgetting inherent in ViT without prior task samples. In the incremental learning of the PlantDiseaseCL dataset across 3-Steps and 5-Steps, our strategy achieved average accuracies of 0.7077 and 0.5661, respectively, surpassing all compared Zero-Exemplar Approaches like LUCIR, SI, MAS, and even outperforming exemplar-based strategies like EEIL and ICaRL. In conclusion, the ViT-TV approach offers robust support for the long-term intelligent development of the agricultural and food industry, especially showcasing significant applicability in continual learning for crop disease image recognition.

First Report of Diplodia quercivora and Neofusicoccum vitifusiforme Associated with Cankers and Necrosis of Holm Oak (Quercus ilex) in Declining Stands in Southern Italy

The emergence of new plant diseases is an increasingly important concern. Climate change is likely to be among the factors causing most of the emerging diseases endangering forest and tree heritage around the world. Such diseases may be caused by latent pathogens or microorganisms cryptically associated with plants. The shift from a non-pathogenic to a pathogenic stage may depend on physiological alterations of the host, environmental changes, and/or stress factors. In some woods of the Salento Peninsula (Apulia Region, Italy), sudden declines of holm oak plants (Quercus ilex L.) have been observed since 2016. The morphological and molecular characterization of representative fungal isolates associated with cankers and necrosis in declining plants indicated that these isolates belong to the Botryosphaeriaceae family, and the most frequent species were Diplodia corticola and Diplodia quercivora, followed by Neofusicoccum vitifusiforme. In artificially inoculated young holm oak plants, both D. corticola and D. quercivora species produced intense and severe subcortical and leaf margin necrosis. N. vitifusiforme, although less aggressive, induced the same symptoms. Our research, in addition to confirming the involvement of D. corticola in olm oak decline, represents the first report of D. quercivora as a new pathogen of Q. ilex in Italy. Furthermore, to the best of our knowledge, we also found N. vitifusiforme as a new pathogen of Q. ilex.

A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates

Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two X. translucens isolates collected from two sites in Colorado, USA, are more aggressive on current wheat and barley varieties compared to older isolates, and we hypothesize that genetic changes between recent and older isolates contribute to the differences in isolate aggressiveness. To test this, we phenotyped and genetically characterized two X. translucens isolates collected from Colorado in 2018, which we designated CO236 (from barley) and CO237 (from wheat). Using pathovar-specific phenotyping and PCR primers, we determined that CO236 belongs to pathovar translucens (Xtt) and CO237 belongs to pathovar undulosa (Xtu). We sequenced the full genomes of the isolates using Oxford Nanopore long-read sequencing, and compared their whole genomes against published X. translucens genomes. This analysis confirmed our pathovar designations for Xtt CO236 and Xtu CO237, and showed that, at the whole-genome level, there were no obvious genomic structural changes between Xtt CO236 and Xtu CO237 and other respective published pathovar genomes. Focusing on pathovar undulosa (Xtu CO237), we then compared putative type III effectors among all available Xtu isolate genomes and found that they were highly conserved. However, there were striking differences in the presence and sequence of various transcription activator-like effectors between Xtu CO237 and published undulosa genomes, which correlate with isolate virulence. Here, we explore the potential implications of the differences in these virulence factors, and provide possible explanations for the increased virulence of recently emerged isolates.

Plant NLR immunity activation and execution: a biochemical perspective

Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.

Phenotypic and genetic characterization of an Avena sativa L. germplasm collection of diverse origin: implications for food-oat breeding in Chile

Oats are known for their nutritional value and also for their beneficial properties on human health, such as the reduction of cholesterol levels and risk of coronary heart disease; they are an important export product for Chile. During the last decade (2010-2022) over 90% of the oat cultivated area in Chile has been covered with Avena sativa L. cv. Supernova INIA. This lack of genetic diversity in a context of climate change could limit the long-term possibility of growing oats in Chile. The present study is a phenotypic and genetic analysis of 132 oat cultivars and pure lines of diverse origin that can be considered as potential breeding material. The germplasm was evaluated for 28 traits and analyzed with 14 SSR markers. The effects of genotypes on phenotype were significant over all traits (P ≤ 0.05). Most traits exhibited moderate to high broad-sense heritability with exceptions such as yield (H2 = 0.27) and hulls staining (H2 = 0.32). Significant undesirable correlations between traits were generally of small biological importance, which is auspicious for achieving breeding objectives. Some of the heritability data and correlations provided here have not been previously reported. The overall phenotypic diversity was high (H' = 0.68 ± 0.18). The germplasm was grouped into three phenotypic clusters, differing in their qualities for breeding. Twenty-six genotypes outperforming Supernova INIA were identified for breeding of conventional food-oats. The genetic diversity of the germplasm was moderate on average (He = 0.58 ± 0.03), varying between 0.32 (AM22) and 0.77 (AME178). Two genetic subpopulations supported by the Structure algorithm exhibited a genetic distance of 0.24, showing low divergence of the germplasm. The diversity and phenotypic values found in this collection of oat genotypes are promising with respect to obtaining genetic gain in the short term in breeding programs. However, the similar genetic diversity, higher phenotypic diversity, and better phenotypic performance of the germplasm created in Chile compared to foreign germplasm suggest that germplasm harboring new genetic diversity will be key to favor yield and quality in new oat cultivars in the long term.

From pandemic to syndemic: microbiota, pregnancy, and environment at a crossroad

Aim: SARS-CoV2 is the latest pandemic that have plagued the socio-health system as an epiphenomenon resulting from planetary resources abuse, crucial for biodiversity. The Anthropocene best defines the present epoch in which human activity irreversibly manipulates intricate and delicate geological and biological balances established over eons. The devastating ecological and socio-economic implications of COVID-19, underline the importance of updating the present pandemic framework to a syndemic. This paper stems from the need to suggest to scientists, doctors, and patients a mission that integrates responsibility from individual to collective health, from present to trans-generational, from human to the entire biotic network. Today's choices are crucial for the perspective on all levels: political, economic, and health as well as cultural.Methods: Research on PubMed and other specific web-sites journal was performed on the topic "Microbiota", "Covid-19", "Pandemic", "Zoonosis", "SARS-CoV-2", "Environmental Pollutants", "Epigenetics", "Fetal Programming", "Human Extinction". Data collected were analysed for an integrative model of interconnection between environment, pregnancy, SARS-CoV-2 infection, and microbiota. Moreover, systematic literature review allowed to summarise in a table information about the worst pandemics that afflicted the human species recently.Results: This paper offers a broad view of the current pandemic starting with pregnancy, the moment when a new life begins and the health trajectories of the unborn child are defined, which will inevitably have repercussions on his well-being. The fundamental role of the biodiversity-rich microbiota in avoiding the development of severe infectious diseases, is therefore highlighted. It is imperative to adjust the current reductionist paradigm based on mostly immediate symptom management towards a broader understanding of the spatial interconnection of ecological niches with human health and the impacts of today's choices on the future. Health and healthcare are elitist rather than egalitarian, therefore focusing on environmental health forces us to make a concerted and systemic effort that challenges political and economic barriers, which are biologically senseless. A healthy microbiota is essential to well-being, both by preventing chronic degenerative conditions, the infectiousness and pathogenicity of bacterial and viral diseases. SARS-CoV-2 should not be an exception. The human microbiota, forged by the first 1,000 days of life, is fundamental in shaping the health-disease trajectories, and by the everlasting exposome that is dramatically affected by the ecological disaster. Individual health is one world health whereas single and global well-being are interdependent in a space-time perspective.Conclusions: Is it not a convenient reductionism not to consider the COVID-19 emergency as a bio-social epiphenomenon of a far more devastating and multi-faceted crisis whose common denominator is the global biotic network loss of which humans are still part?

A systematic review of the intercontinental movement of unregulated African meat imports into and through European border checkpoints

There is an urgent need for biosurveillance of unregulated African meat imports at border points of entry in destination markets. This is underscored by recent pandemics linked to exotic wildlife products. Our objective was to catalog the quantity of meat that is informally transported from Africa into and through Europe often without any veterinary or sanitary checks. We searched and included peer-reviewed studies that contained data on the intercontinental movement of unregulated meat from the African continent. This was followed by an investigation of the reported contamination of such meat. We included fifteen airport studies with limited data on this topic. The references included in this review describe the quantity of meat found at border inspection posts and the presence of pathogens. Disease-causing pathogens were found to be present, and the results are organized into bacteria, virus, and parasite categories. The species of animal meat found in this review were linked to CITES-protected species some of which are known reservoir hosts for infectious diseases. This represents a potential and unquantified human health risk to populations along the supply chain, and a loss to biodiversity in supply countries. Meat samples described in this review were primarily found opportunistically by Customs officials, indicating that any estimate of the total quantities passing undetected through border checkpoints must remain tentative, and cannot rule out the possibility that it is indeed considerably higher. We propose a template for future studies regarding African meat imports at border points of entry. The result of this review illustrates a gap in knowledge and lacunae regarding the amount of unregulated African meat imports worldwide, the pathogens it may contain, and the resulting biodiversity loss that occurs from the intercontinental movement of this meat.

Discovery of novel salicylaldehyde derivatives incorporating an α-methylene-γ-butyrolactone moiety as fungicidal agents

BACKGROUND

Plant diseases caused by phytopathogenic fungi and oomycetes pose a serious threat to ensuring crop yield and quality. Finding novel fungicidal candidates based on natural products is one of the critical methods for developing effective and environmentally friendly pesticides. In this study, a series of salicylaldehyde derivatives containing an α-methylene-γ-butyrolactone moiety were designed, synthesized, and their fungicidal activities were evaluated.

RESULTS

The bioassay studies indicated that compound C3 displayed an excellent in vitro activity against Rhizoctonia solani with a half-maximal effective concentration (EC50 ) value of 0.65 μg/mL, higher than that of pyraclostrobin (EC50  = 1.44 μg/mL) and comparable to that of carbendazim (EC50  = 0.33 μg/mL). For Valsa mali and Phytophthora capsici, compound C3 also showed good fungicidal activities with EC50 values of 0.91 and 1.33 μg/mL, respectively. In addition, compound C3 exhibited promising protective in vivo activity against R. solani (84.1%) at 100 μg/mL, which was better than that of pyraclostrobin (78.4%). The pot experiment displayed that compound C3 had 74.8% protective efficacy against R. solani at 200 μg/mL, which was comparable to that of validamycin (78.2%). The antifungal mode of action research indicated that compound C3 could change the mycelial morphology and ultrastructure, increase cell membrane permeability, affect respiratory metabolism by binding to complex III, and inhibit the germination and formation of sclerotia, thereby effectively controlling the disease.

CONCLUSION

The present study provides support for the application of these salicylaldehyde derivatives as promising potential pesticides with remarkable and broad-spectrum fungicidal activities against phytopathogenic fungi and oomycetes in crop protection. © 2023 Society of Chemical Industry.

Genome Mining from Agriculturally Relevant Fungi Led to a d-Glucose Esterified Polyketide with a Terpene-like Core Structure

Comparison of biosynthetic gene clusters (BGCs) found in devastating plant pathogens and biocontrol fungi revealed an uncharacterized and conserved polyketide BGC. Genome mining identified the associated metabolite to be treconorin, which has a terpene-like, trans-fused 5,7-bicyclic core that is proposed to derive from a (4 + 3) cycloaddition. The core is esterified with d-glucose, which derives from the glycosidic cleavage of a trehalose ester precursor. This glycomodification strategy is different from the commonly observed glycosylation of natural products.

Streptomyces as a promising biological control agents for plant pathogens

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

A Decade of Hidden Phytoplasmas Unveiled Through Citizen Science

Climate change is impacting agriculture in many ways, and a contribution from all is required to reduce the imminent losses related to it. Recently, it has been shown that citizen science could be a way to trace the impact of climate change. However, how can citizen science be applied in plant pathology? Here, using as an example a decade of phytoplasma-related diseases reported by growers, agronomists, and citizens in general, and confirmed by a government laboratory, we explored how to better value plant pathogen monitoring data. Through this collaboration, we found that in the last decade, 34 hosts have been affected by phytoplasmas; 9, 13, and 5 of these plants were, for the first time, reported phytoplasma hosts in eastern Canada, all of Canada, and worldwide, respectively. Another finding of great impact is the first report of a 'Candidatus Phytoplasma phoenicium'-related strain in Canada, while 'Ca. P. pruni' and 'Ca. P. pyri' were reported for the first time in eastern Canada. These findings will have a great impact on the management of phytoplasmas and their insect vectors. Using these insect-vectored bacterial pathogens, we show the need for new strategies that can allow fast and accurate communication between concerned citizens and those institutions confirming their observations.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

MS-Net: a novel lightweight and precise model for plant disease identification

The rapid development of image processing technology and the improvement of computing power in recent years have made deep learning one of the main methods for plant disease identification. Currently, many neural network models have shown better performance in plant disease identification. Typically, the performance improvement of the model needs to be achieved by increasing the depth of the network. However, this also increases the computational complexity, memory requirements, and training time, which will be detrimental to the deployment of the model on mobile devices. To address this problem, a novel lightweight convolutional neural network has been proposed for plant disease detection. Skip connections are introduced into the conventional MobileNetV3 network to enrich the input features of the deep network, and the feature fusion weight parameters in the skip connections are optimized using an improved whale optimization algorithm to achieve higher classification accuracy. In addition, the bias loss substitutes the conventional cross-entropy loss to reduce the interference caused by redundant data during the learning process. The proposed model is pre-trained on the plant classification task dataset instead of using the classical ImageNet for pre-training, which further enhances the performance and robustness of the model. The constructed network achieved high performance with fewer parameters, reaching an accuracy of 99.8% on the PlantVillage dataset. Encouragingly, it also achieved a prediction accuracy of 97.8% on an apple leaf disease dataset with a complex outdoor background. The experimental results show that compared with existing advanced plant disease diagnosis models, the proposed model has fewer parameters, higher recognition accuracy, and lower complexity.

Apple CRISPR-Cas9-A Recipe for Successful Targeting of AGAMOUS-like Genes in Domestic Apple

Fruit trees and other fruiting hardwood perennials are economically valuable, and there is interest in developing improved varieties. Both conventional breeding and biotechnology approaches are being utilized towards the goal of developing advanced cultivars. Increased knowledge of the effectiveness and efficiency of biotechnology approaches can help guide use of the CRISPR gene-editing technology. Here, we examined CRISPR-Cas9-directed genome editing in the valuable commodity fruit tree Malus x domestica (domestic apple). We transformed two cultivars with dual CRISPR-Cas9 constructs designed to target two AGAMOUS-like genes simultaneously. The main goal was to determine the effectiveness of this approach for achieving target gene changes. We obtained 6 Cas9 control and 38 independent CRISPR-Cas9 events. Of the 38 CRISPR-Cas9 events, 34 (89%) had gene edits and 14 (37%) showed changes to all alleles of both target genes. The most common change was large deletions, which were present in 59% of all changed alleles, followed by small deletions (21%), small insertions (12%), and a combination of small insertions and deletions (8%). Overall, a high rate of successful gene alterations was found. Many of these changes are predicted to cause frameshifts and alterations to the predicted peptides. Future work will include monitoring the floral development and floral form.

The potential of UAV and very high-resolution satellite imagery for yellow and stem rust detection and phenotyping in Ethiopia

Very high (spatial and temporal) resolution satellite (VHRS) and high-resolution unmanned aerial vehicle (UAV) imagery provides the opportunity to develop new crop disease detection methods at early growth stages with utility for early warning systems. The capability of multispectral UAV, SkySat and Pleiades imagery as a high throughput phenotyping (HTP) and rapid disease detection tool for wheat rusts is assessed. In a randomized trial with and without fungicide control, six bread wheat varieties with differing rust resistance were monitored using UAV and VHRS. In total, 18 spectral features served as predictors for stem and yellow rust disease progression and associated yield loss. Several spectral features demonstrated strong predictive power for the detection of combined wheat rust diseases and the estimation of varieties' response to disease stress and grain yield. Visible spectral (VIS) bands (Green, Red) were more useful at booting, shifting to VIS-NIR (near-infrared) vegetation indices (e.g., NDVI, RVI) at heading. The top-performing spectral features for disease progression and grain yield were the Red band and UAV-derived RVI and NDVI. Our findings provide valuable insight into the upscaling capability of multispectral sensors for disease detection, demonstrating the possibility of upscaling disease detection from plot to regional scales at early growth stages.

Climate change impacts on plant pathogens, food security and paths forward

Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.

Next-generation bulked segregant analysis for Breeding 4.0

Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method for functional cloning, its low throughput cannot satisfy the current need for crop breeding and food security. Here, we review the rationale and development of conventional BSA and discuss its strengths and drawbacks. We then propose next-generation BSA (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, and the use of machine learning. NG-BSA increases the resolution of genetic mapping and throughput for cloning quantitative trait genes (QTGs) and optimizes candidate gene selection while providing a means to elucidate the interaction network of QTGs. The ability of NG-BSA to efficiently batch-clone QTGs makes it an important tool for dissecting molecular mechanisms underlying various traits, as well as for the improvement of Breeding 4.0 strategy, especially in targeted improvement and population improvement of crops.

Pathogenesis and Disease Control in Crops: The Key to Global Food Security

Plant diseases are a major threat to global food security [...].

Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data

High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Long-Term Monitoring of Aphid-Transmitted Viruses in Melon and Zucchini Crops: Genetic Diversity and Population Structure of Cucurbit Aphid-Borne Yellows Virus and Watermelon Mosaic Virus

Understanding the emergence and prevalence of viral diseases in crops requires the systematic epidemiological monitoring of viruses, as well as the analysis of how ecological and evolutionary processes combine to shape viral population dynamics. Here, we extensively monitored the occurrence of six aphid-transmitted viruses in melon and zucchini crops in Spain for 10 consecutive cropping seasons between 2011 and 2020. The most prevalent viruses were cucurbit aphid-borne yellows virus (CABYV) and watermelon mosaic virus (WMV), found in 31 and 26% of samples with yellowing and mosaic symptoms. Other viruses, such as zucchini yellow mosaic virus, cucumber mosaic virus, Moroccan watermelon mosaic virus, and papaya ring spot virus, were detected less frequently (<3%) and mostly in mixed infections. Notably, our statistical analysis showed a significant association between CABYV and WMV in melon and zucchini hosts, suggesting that mixed infections might be influencing the evolutionary epidemiology of these viral diseases. We then carried out a comprehensive genetic characterization of the full-length genome sequences from CABYV and WMV isolates by using the Pacific Biosciences single-molecule real-time (PacBio) high-throughput technology to assess the genetic variation and structure of their populations. Our results showed that the CABYV population displayed seven codons under positive selection, and although most isolates clustered in the Mediterranean clade, a subsequent analysis of molecular variance revealed a significant, fine-scale temporal structure, which was in part explained by the level of the variance between isolates from single and mixed infections. In contrast, the WMV population genetic analysis showed that most of the isolates grouped into the Emergent clade, with no genetic differentiation and under purifying selection. These results underlie the epidemiological relevance of mixed infections for CABYV and provide a link between genetic diversity and CABYV dynamics at the whole-genome level.

Lanthanum Silicate Nanomaterials Enhance Sheath Blight Resistance in Rice: Mechanisms of Action and Soil Health Evaluation

In the current study, foliar spray with lanthanum (La) based nanomaterials (La10Si6O27 nanorods, La10Si6O27 nanoparticle, La(OH)3 nanorods, and La2O3 nanoparticle) suppressed the occurrence of sheath blight (Rhizoctonia solani) in rice. The beneficial effects were morphology-, composition-, and concentration-dependent. Foliar application of La10Si6O27 nanorods (100 mg/L) yielded the greatest disease suppression, significantly decreasing the disease severity by 62.4% compared with infected controls; this level of control was 2.7-fold greater than the commercially available pesticide (Thifluzamide). The order of efficacy was as follows: La10Si6O27 nanorods > La10Si6O27 nanoparticle > La(OH)3 nanorods > La2O3 nanoparticle. Mechanistically, (1) La10Si6O27 nanorods had greater bioavailability, slower dissolution, and simultaneous Si nutrient benefits; (2) transcriptomic and metabolomic analyses revealed that La10Si6O27 nanorods simultaneously strengthened rice systemic acquired resistance, physical barrier formation, and antioxidative systems. Additionally, La10Si6O27 nanorods improved rice yield by 35.4% and promoted the nutritional quality of the seeds as compared with the Thifluzamide treatment. A two-year La10Si6O27 nanorod exposure had no effect on soil health based on the evaluated chemical, physical, and biological soil properties. These findings demonstrate that La based nanomaterials can serve as an effective and sustainable strategy to safeguard crops and highlight the importance of nanomaterial composition and morphology in terms of optimizing benefit.

On the way to potential antifungal compounds: synthesis and in vitro activity of 2-benzofuranylacetic acid amides

Crop losses caused by microbial infections are a significant global issue, especially in tropical regions. The development of novel antimicrobial agents, particularly antifungal agents, has been explored from various perspectives, including chemical synthesis. However, conventional approaches typically involve synthesizing new and potent compounds on a small scale (a few milligrams), making the scale-up of the reaction a major challenge. In this manuscript, we present a method for the synthesis of new and active (against Fusarium oxysporum) benzofuranyl acetic acid amides. Our strategy allows us to synthesize the key precursor on the gram scale, enabling the production of sufficient quantities of other active compounds within short timeframes for conducting biological studies. All the reactions used in this manuscript are recognized by their industrial application.

Spatial spread of infectious diseases with conditional vector preferences

We explore the spatial spread of vector-borne infections with conditional vector preferences, meaning that vectors do not visit hosts at random. Vectors may be differentially attracted toward infected and uninfected hosts depending on whether they carry the pathogen or not. The model is expressed as a system of partial differential equations with vector diffusion. We first study the non-spatial model. We show that conditional vector preferences alone (in the absence of any epidemiological feedback on their population dynamics) may result in bistability between the disease-free equilibrium and an endemic equilibrium. A backward bifurcation may allow the disease to persist even though its basic reproductive number is less than one. Bistability can occur only if both infected and uninfected vectors prefer uninfected hosts. Back to the model with diffusion, we show that bistability in the local dynamics may generate travelling waves with either positive or negative spreading speeds, meaning that the disease either invades or retreats into space. In the monostable case, we show that the disease spreading speed depends on the preference of uninfected vectors for infected hosts, but also on the preference of infected vectors for uninfected hosts under some circumstances (when the spreading speed is not linearly determined). We discuss the implications of our results for vector-borne plant diseases, which are the main source of evidence for conditional vector preferences so far.

Starving the enemy: how plant and microbe compete for sugar on the border

As the primary energy source for a plant host and microbe to sustain life, sugar is generally exported by Sugars Will Eventually be Exported Transporters (SWEETs) to the host extracellular spaces or the apoplast. There, the host and microbes compete for hexose, sucrose, and other important nutrients. The host and microbial monosaccharide transporters (MSTs) and sucrose transporters (SUTs) play a key role in the "evolutionary arms race". The result of this competition hinges on the proportion of sugar distribution between the host and microbes. In some plants (such as Arabidopsis, corn, and rice) and their interacting pathogens, the key transporters responsible for sugar competition have been identified. However, the regulatory mechanisms of sugar transporters, especially in the microbes require further investigation. Here, the key transporters that are responsible for the sugar competition in the host and pathogen have been identified and the regulatory mechanisms of the sugar transport have been briefly analyzed. These data are of great significance to the increase of the sugar distribution in plants for improvement in the yield.