Apple (Malus domestica Borkh.) is one of the most widely consumed fruit crops globally, with an annual production of approximately 83.98 million metric tons in 2024-25. However, its productivity and fruit quality are severely affected by Alternaria leaf blotch, caused by Alternaria alternata, a major fungal pathogen capable of inducing up to 85% leaf defoliation. Despite its economic importance, the molecular basis of apple-Alternaria interactions remain poorly understood. Comparative temporal transcriptome profiling was performed on susceptible ‘Red Delicious’ leaves at 24 and 96 h post-inoculation (hpi) to characterize host responses to A. alternata. A total of 2457 and 2813 differentially expressed genes (DEGs) (|log2FC| ≥ 2, adjusted p < 0.05) were identified at 24 and 96 hpi, respectively. The transcriptomic response involved defense-associated signaling, transcription factors, pathogenesis-related (PR) proteins, and hormone-responsive genes. KEGG analysis identified MAPK signaling, plant-pathogen interaction, hormone signal transduction, and phenylpropanoid biosynthesis among the major enriched pathways. WRKY transcription factors, particularly WRKY33 and WRKY75, showed strong induction, while PR1 and PR10 genes were prominently upregulated. Ethylene-associated genes exhibited comparatively strong transcriptional responses, although this represents a transcriptome-based inference rather than direct evidence of hormone accumulation. The simultaneous induction and suppression of different defense-associated genes suggests dynamic but potentially insufficient defense responses in the susceptible cultivar. Expression patterns of 20 defense-related genes were further evaluated by qRT-PCR. Overall, this study provides temporal insights into the transcriptional reprogramming of ‘Red Delicious’ during A. alternata infection and identifies candidate genes and pathways for future functional characterization and disease-resistance improvement.
The escalating threat of bacterial plant pathogens, coupled with widespread resistance to conventional copper bactericides and agricultural antibiotics, necessitates innovative agrochemical alternatives. While chitosan-metal nanocomposites (Cs-Metal NCs) present a transformative frontier in plant protection, existing literature frequently conflates these advanced nano-formulations with unmodified bulk chitosan and relies on oversimplified, deterministic mechanistic models. This critical review systematically decouples Cs-Metal NCs from bulk biopolymers, elucidating how nanoscale coordination chemistry dictates biological efficacy. Moving beyond the traditional Gram-positive/Gram-negative dichotomy, it was critically analyzed how specific transition metal dopants (Cu, Ag, Zn, Mg) overcome physiological barriers, including extracellular polymeric substance matrices, biofilm architecture, and stationary-phase dormancy. Furthermore, the dual elicitation paradigm was explored, wherein the chitosan backbone acts as a microbe-associated molecular pattern while controlled metal release induces chemical eustress, synergistically priming robust systemic acquired resistance in host plants. This synthesis also rigorously categorizes current in silico computational models, distinguishing phytopathogen-specific rational design from indirectly relevant clinical proxies and transparently addresses algorithmic limitations. Finally, it was provided a critical evaluation of commercial translational hurdles, the "reality check", assessing multitrophic ecotoxicology, formulation inconsistencies, and the frequently overlooked selection risk of pathogen adaptive tolerance under long-term field application. Ultimately, advancing Cs-Metal NCs from controlled in vitro promise to sustainable, field-validated integrated pest management frameworks require pivoting toward realistic pathosystems, complex soil microbiome dynamics, and standardized physicochemical parameters.
The rhizosphere microbiota has emerged as a promising resource for the eco-friendly management of plant parasitic nematodes (PPN). Beneficial microorganisms inhabiting the rhizosphere and plant tissues suppress through multiple mechanisms, including direct parasitism, production of nematicidal metabolites and volatile organic compounds, secretion of hydrolytic enzymes, competition for ecological niches, biofilm formation, and induction of systemic resistance, while simultaneously promoting plant growth and improving soil health. This review discusses recent advances in suppression of PPNs, with particular emphasis on microbiota engineering and the transition from single inoculants to synthetic microbial communities (SynComs). It further discusses the application of high-throughput multi-omics approaches, including metagenomics and metabolomics, to unravel microbial diversity, functional interactions, and nematode-suppressive mechanisms. Emerging technologies such as artificial intelligence and machine learning for predictive microbiota analysis, microbial consortium design, and precision nematode management are also highlighted. In addition, current challenges related to field performance, formulation stability, microbial establishment, and commercialization are critically discussed. Finally, future perspectives on integrating microbiota engineering, systems biology, and digital agriculture are presented to develop resilient, environmentally sustainable, and climate-smart strategies for PPN long-term management.
Plant diseases caused by microbial pathogens in arid and semi-arid agroecosystems present growing challenges to sustainable crop production, particularly under chronic abiotic stress and increasing climate variability. In the United Arab Emirates (UAE) and the broader Gulf Cooperation Council (GCC) region, plant health is shaped by extreme heat, water scarcity, soil salinity, and intensified agricultural practices. Despite these pressures, phytopathological knowledge in the region remains fragmented across pathogen groups.In this review, we synthesize current evidence on bacterial, fungal and oomycete, viral and viroid, phytoplasma, and plant-parasitic nematode pathogens and disease-associated taxa affecting crops in the UAE and the GCC, with a particular focus on date palm (Phoenix dactylifera L.) as a model arid perennial system. This crop is used to illustrate mechanisms of chronic disease development in long-lived plants under arid conditions, while broader crop examples are included to contextualize regional pathogen diversity. Using a host-centered, multi-kingdom approach that considers bacteria, fungi, viruses, viroids, and phytoplasmas together, we distinguish experimentally supported causal pathogens from field-associated taxa, secondary colonizers, and hypothesized co-infection scenarios. We examine disease prevalence, pathogenic mechanisms, and diagnostic challenges under arid conditions, while emphasizing that direct evidence for synergistic multi-kingdom interactions in regional date-palm systems remains limited. We further evaluate the role of climate change in modifying disease epidemiology and discuss emerging threats associated with transboundary pathogen movement. We emphasize the need for accurate diagnostics, particularly molecular tools and high-throughput sequencing, to detect underrecognized pathogens and mixed infections and to support evidence-based management. Finally, we discuss integrated disease management and biocontrol strategies suited to arid agroecosystems and outline priority research directions for advancing phytopathological surveillance and sustainable disease control in the UAE, the GCC, and other regions facing increasing aridity.
Viruses are among the most prevalent pathogens threatening plants. As a defense mechanism, plants have evolved a sequence-specific antiviral strategy known as RNA silencing. After infection, some plants undergo recovery, during which newly emerging leaves become asymptomatic and resistant to further infection. To identify mechanisms that contribute to recovery in addition to RNA silencing, we studied transgenic tobacco plants expressing the complete NIa cistron of Tobacco etch virus (TEV) that recover three weeks after inoculation. Using in situ hybridization with an NIa probe, qRT-PCR targeting CP and NIa, and back-inoculation assays, we found that the NIa-hybridizing signal persisted in the stem and leaf vasculature. The probe detects both viral and transgene-derived RNA, thereby showing the spatial distribution of NIa-hybridizing RNA. The RNA silencing-associated genes DCL2 and RDR6 were upregulated in recovered leaves, whereas the endogenous silencing suppressor rgs-CaM was upregulated in stems. Callose-related genes and callose deposition at plasmodesmata were also increased in recovered leaves. Our findings indicate that recovery is compartmentalized: a marked reduction in total NIa RNA, consistent with sequence-specific RNA silencing, is associated with the loss of detectable CP RNA from recovered leaf extracts, whereas CP RNA and infectivity remain detectable in stem tissue. In recovered leaves, callose deposition at plasmodesmata is associated with this tissue-specific restriction of viral movement and may act alongside RNA silencing, suggesting that recovery may involve both sequence-specific RNA silencing and a tissue-level restriction of viral spread.
