Can waste serve as a source of known or novel molecules for plant disease management? This review explores this question, which is closely linked to the necessity of mitigating the environmental impact of agriculture, specifically in terms of waste generation and greenhouse gas emissions. Furthermore, it addresses the increasing demand for safer, environmentally friendly alternatives to ensure sustainable plant production and protection. To satisfy these needs, research efforts over the past few decades have primarily focused on biocontrol strategies, with the valorization of waste being addressed only recently. Different approaches have been applied for extracting bioactive molecules from waste, ranging from green chemistry to microbial fermentation. We discuss secondary metabolites, elicitors, and biosurfactants obtained chemically and from fermentation. Microorganisms growing on waste can produce biomass or spores [bioactive ingredients of plant-protection products (PPPs)] and facilitate the extraction of active compounds. Although the production of spores on waste material is now well-established on an industrial scale, the extraction of biologicals from waste and/or their production through fermentation are still at the experimental stage. The growing knowledge on the bioactivity of agri-food waste-derived molecules against phytopathogens is paving the way for the development of new PPPs suitable for integrated pest management. The waste-based PPPs pipeline described here shows strong potential to generate both established and novel, regulation-compliant compounds without sacrificing disease-control efficacy.
Plant-parasitic nematodes are increasingly important in turfgrass systems due to changes in public demands for high turfgrass quality standards and low environmental impacts, loss of heavy metal pesticides along with the development of new nematode management tools, and the expanding range of some highly virulent species. This has subsequently increased demand for turfgrass nematode diagnosis, and many diagnostic labs struggle with proper interpretation of these samples. In this review, we discuss some of the factors contributing to the increased demand for turfgrass nematode diagnostics and the challenges of providing meaningful results. We also provide a review of the different families of plant-parasitic nematodes associated with turfgrasses in North America and their relative importance.
Airborne dispersal enables plant pathogens to travel across fields, regions, and continents, fueling rapid epidemics and emerging disease threats. Biosurveillance, the systematic monitoring of airborne inoculum, offers the opportunity to detect pathogens before symptoms appear and informs timely, risk-based management. Recent advances in air sampling, molecular diagnostics, metagenomics, and imaging technologies have expanded the scale and resolution of pathogen monitoring, from single-species qPCR assays to community-level aerobiome surveys. Integration of biosurveillance data with decision-support systems, remote sensing, and artificial intelligence is transforming early-warning capabilities and providing novel insights into pathogen ecology, evolution, and fungicide resistance. Yet major challenges remain, including assay standardization, data interpretation, and translation into actionable tools for growers. This review synthesizes current approaches, highlights case studies in which biosurveillance has advanced disease management, and outlines future directions toward coordinated surveillance networks and precision agriculture applications.
Phytophthora infestans killed the potato crop in Ireland in 1845, leading to widespread famine and the death of more than one million people. Historic herbarium specimens from the famine era were used to understand the pathogen's biology and track its global spread, providing a valuable resource for research. Historic outbreaks in the United States and Europe were caused by the FAM-1 lineage, whereas the US-1 lineage spread later. The famine lineage was basal in the phylogeny and ancestral to modern US-1, Mexican, and globally aggressive lineages. An admixture between the famine lineage and the Andean species Phytophthora andina was revealed, indicating a South American origin of the disease. Temporal changes in the presence and abundance of virulence genes were observed in historic compared to modern genomes. Expansion in effector abundance occurred as new genotypes emerged in the mid-twentieth century. Disease surveillance and genotyping on a global scale have helped to inform disease management.
Some plant-beneficial microbes, including bacteria and fungi, can induce plant defense, enabling plants to resist pathogen infections. Successful defense elicitation depends on compatible host-microbe interactions at multiple stages. The initial interaction begins with plant root exudates, which contain chemical cues that attract beneficial microbes by enhancing their motility, biofilm formation, and expression of symbiosis- and immunity-related genes. In turn, these microbes produce a diverse array of immune elicitors-such as proteins, carbohydrates, lipids, and volatile compounds-that are perceived by plants through various mechanisms. Some elicitors are recognized by membrane-bound pattern recognition receptors, whereas others interact with the plant plasma membrane or cytoplasmic targets such as MYB72 and LOX3. These interactions can either trigger local pattern-triggered immunity, characterized by reactive oxygen species production and activation of the mitogen-activated protein kinase signaling pathway, or generate long-distance signals such as oxylipins that induce systemic resistance in distal tissues. A central outcome of these interactions is induced systemic resistance, which primes plants for a heightened immune state, enabling faster and stronger defense responses upon a subsequent pathogen challenge. In some cases, beneficial microbes can also trigger salicylic acid-mediated systemic acquired resistance, particularly enhancing resistance against biotrophic pathogens. Furthermore, beneficial microbes must balance immune activation and immune evasion by suppressing microbe-associated molecular pattern-triggered immune responses and avoiding the formation of hyperbiofilm, which allows them to establish a long-term symbiotic relationship with the host.
Climate change is fundamentally reshaping forest disease dynamics through direct effects on pathogen biology and indirect impacts on host physiology. Rising temperatures, altered precipitation patterns, and extreme weather events are driving disease emergence by disrupting ecological relationships between trees and their microbial associates. This review examines how climate change compounds biotic and abiotic risks to forest health, distinguishing between climate-pathogen diseases, where climatic shifts directly favor pathogen activity, and climate-stress diseases, where physiological stress predisposes trees to decline. We explore the continuum from native pathogens gaining new opportunities to exotic pathogens establishing in previously unsuitable environments while considering distinctions among endophytes and latent and nonlatent pathogens. The review emphasizes critical knowledge gaps and highlights emerging research directions, including integration of genomics, remote sensing, and predictive modeling for disease surveillance, adaptive forest management strategies balancing disease mitigation with climate adaptation and new solutions for enhancing forest resilience under accelerating environmental change.
Forest pathogens have repeatedly restructured ecosystems in the Northern Hemisphere, where epidemics such as chestnut blight, Dutch elm disease, and sudden oak death eliminated foundation species and reshaped landscapes. In contrast, the Southern Hemisphere, buffered by geographic isolation, unique floras, and historically lower trade volumes, experienced comparatively few incursions until recent decades. These barriers are rapidly eroding due to globalization, climate change, and the expansion of industrial plantation forestry dominated by exotic species of Pinus and Eucalyptus. These vast monocultures with low genetic diversity have created highly susceptible production systems that can amplify epidemic spread and act as sources of novel pathogen emergence. Drawing on lessons from the Northern Hemisphere, this review highlights the escalating risk of forest epidemics in the Southern Hemisphere and calls for proactive, coordinated responses. Stringent phytosanitary standards, advanced diagnostic techniques, and risk-optimized surveillance must be paired with collaborative breeding programs that prioritize resistance in high-risk hosts. At the same time, international cooperation across science, policy, industry, and communities is essential to strengthen prevention, support early detection, and enable rapid response. The resilience of Southern Hemisphere forests, both native and plantations, will depend on shifting from reactive management toward integrated, globally coordinated strategies that recognize the shared nature of pathogen threats.
Plant diseases threaten global food security, causing up to 40% crop yield losses and more than $220 billion in annual economic damage. This review synthesizes recent advances in understanding the genomic variations and mutational events underlying plant-pathogen interactions and durable plant disease resistance. Key insights into evolutionary dynamics, genetic variability, and coadaptive strategies reveal the complexity of host-pathogen relationships and the implications for developing durable disease resistance. Integrative approaches combining genome-wide association studies and functional genomics have uncovered the polygenic and epistatic architecture of quantitative resistance. Advances in pan-genomics and high-throughput sequencing have revealed extensive genetic variability in cultivated/elite germplasm and wild relatives. Emerging technologies, including gene editing, multi-omics, and machine learning, enable predictive modeling of resistance traits and support evolution that informs plant breeding strategies. Collectively, these advances provide a robust framework for developing durable resistance and sustainable crop protection in the face of global agricultural challenges.
Forests are central to planetary health but are increasingly challenged by emerging diseases driven by climate change, global trade, and anthropogenic disturbance. Despite the apparent resilience of long-lived, genetically diverse tree hosts, forest ecosystems have repeatedly experienced landscape-level pathogen-driven transformations. Advances in genomics, transcriptomics, and functional biology have transformed our understanding of how fungal and oomycete pathogens interact with their hosts across a continuum of lifestyles, from saprotrophy and necrotrophy to biotrophy. Here, we synthesize insights from comparative and population genomics and functional studies across diverse forest pathosystems to examine the traits that characterize successful tree pathogens. We highlight how lifestyle plasticity, adaptations to woody tissues, vector-mediated transmission, and biotrophic stealth enable pathogens to colonize perennial hosts and persist over long temporal scales. We further examine how genome plasticity, hybridization, and horizontal gene transfer generate adaptive potential that often outpaces host evolutionary responses under current environmental change. Finally, we discuss emerging genomic tools, including biosurveillance, machine learning-based classification, and genome editing, that are beginning to link genotype to phenotype and inform assessments of disease risk. By integrating genomic, ecological, and evolutionary perspectives, this review outlines general principles governing forest pathogen success and identifies priorities for future research aimed at improving understanding, early detection, and management of forest diseases in a changing world.
The outcome of infection can be seen as a race between the pathogen and the plant immune system. In this review, we use the case study of Xylella fastidiosa (Xf) and explain how the bacterium exploits its slow and fastidious growth to remain below detection thresholds, thereby delaying immune activation. Its self-limiting behavior in the sessile state provides a temporal window for transitioning into a more exploratory lifestyle, enabling systemic colonization of the host. As bacterial populations expand, vessel occlusion and immune overactivation at late stages occur, often propagating beyond directly infected tissues, leading to hydraulic collapse and drought-like symptoms. We highlight how Xf's adaptations to a nutrient-poor and rapid-flow environment contribute to its persistence. Furthermore, we discuss how resistant plant genotypes, possessing broader or more sensitive repertoires of immune receptors, can detect the pathogen earlier and restrict its systemic spread in the xylem. Understanding the dynamics of these "catch me if you can" strategies may guide novel approaches to reduce Xf survival and mitigate disease progression in susceptible crops while also providing broader insights into plant responses and the infection strategies of other xylem-inhabiting microbes.
This review aims to fill a critical gap-phytosanitation methods for inert surfaces, such as farming equipment, containers, tools, and shoes, to mitigate plant pathogen establishment and expansion. Although a core component to food system security and ecosystem stability, especially for mitigating emerging pathogen impacts, this is one of the least studied disease management tools and often lacks robust science-based practices. We herein synthesize what is known about inert surface phytosanitation practices across diverse microbiological and plant pest systems and highlight opportunities for improving both phytosanitation practices and approaches used for phytosanitation science. Basic frameworks are first established for the types of plant pathogen propagules that are spread on surfaces and dispersal risks posed by key inert surface types. This is followed by a discussion of primary surface phytosanitation methods, including physical, chemical, and heat-based approaches. Case studies of nursery/greenhouse and farm equipment phytosanitation are used to demonstrate both systems-strategies for application of phytosanitation best management practices and methods for developing science-based practices using the hazard analysis for critical control points (HACCP) approach. Opportunities for growth discussed throughout include the use of pathogen-specific analyses and epidemiological modeling to improve phytosanitation science and engineering advancements to make phytosanitation practices more efficient. Taken together, it is hoped that this synthesis can both function as a resource for practitioners looking to develop and improve phytosanitation practices and provide impetus for innovation.
Viruses are obligate intracellular parasites that rely on their hosts for the cellular machinery necessary for their replication and transmission to new hosts. Viruses are therefore invaluable for illuminating numerous facets of their hosts' biology. Plant viruses take advantage of the cell-to-cell connectivity provided by plasmodesmata for their movement from sites of replication to the vasculature for eventual systemic dissemination in their plant hosts, a strategy distinct from viruses that use animal and fungal hosts. Given their reliance on plasmodesmata for successful infection and spread in plant hosts, viruses remain powerful tools for probing plasmodesmal function and cell wall processes. The structure and function of plasmodesmata as well as the factors that contribute to plasmodesmal permeability are discussed here from the perspective of plasmodesmata as integral cell wall components. The relationship between the cell wall and plasmodesmata and how viruses affect both is also examined. The possibility that plasmodesmata are intriguing targets for designing novel strategies for crops with improved resistance to pathogens is also addressed.
Extracellular interactions are pivotal in the plant-pathogen arms race. Fungal, bacterial, and oomycete pathogens manipulate the apoplast to control pH, water soaking, sugar levels, and nutrient availability. Plants respond to infection with an oxidative burst and secrete toxic metabolites and harmful hydrolases, but adapted pathogens have evolved intricate ways to disarm reactive and toxic plant metabolites and inhibit or degrade hydrolases. Pathogens also avoid their recognition by hiding, degrading, or modifying their elicitors and disabling cell surface receptors in various ways. In this review, we summarize our current knowledge on fascinating offense and counter-defense mechanisms in extracellular plant-pathogen interactions.
The Benyviridae family encompasses multipartite soil-borne phytoviruses characterized by rod-shaped virions and positive single-stranded RNA genomes. The family is mostly known for its type species, the beet necrotic yellow vein virus, the causal agent of rhizomania on sugar beet. However, the recent description of candidate Benyviridae species and "beny-like" sequences suggests a far greater diversity than previously recognized. Also, their increasing relevance in agriculture has drawn attention to this family of viruses. In this review, we provide a comparative analysis of Benyviridae viruses, including newly identified emerging relatives. We highlight recent advances in understanding their diversity, pathogenicity, and interaction with plant hosts and their plasmodiophorid vectors, Polymyxa spp., that remain poorly characterized. Finally, we identify critical knowledge gaps and exciting opportunities-particularly in vector biology, host interactions, and the ecological dynamics of viral spread-that will shape the research ahead.
Cross-protection, discovered nearly a century ago, is a biological control method used to manage viral plant diseases. It is usually defined as a phenomenon in which a primary infection of a host by a pathogen (e.g., a mild strain) prevents its subsequent infection by a genetically related one (e.g., a severe related strain). Despite the long-standing research interest in this phenomenon from both a fundamental and an applied perspective, the mechanisms and factors-both viral and host-derived-underlying this phenomenon remain unclear, limiting its broader application. Proposed mechanisms include RNA silencing and potential roles of viral proteins, but inconsistent terminology and mixed evidence in the literature have made conclusions difficult. This review critically analyzes existing studies on plant virus cross-protection, summarizing common characteristics across systems and comparing them with proposed mechanisms. The findings suggest that cross-protection may result from different mechanisms that vary depending on the specific plant-virus interactions.
Beech leaf disease (BLD) has emerged as a significant threat to beech forests in North America, causing the widespread decline of American beech while posing a potential threat to other beech species worldwide. BLD has drawn considerable attention due to its rapid spread and the visible decline it causes in beech trees. Since its first detection, the disease has rapidly expanded its geographic range, underscoring the urgent need for a comprehensive understanding of its etiology and epidemiology. This disease is characterized by interveinal dark banding of the leaf, bud abortion, and progressive canopy thinning. These symptoms are associated with the infection of Litylenchus crenatae, a newly described foliar nematode native to Asia. This nematode exhibits a sophisticated parasitic interaction with beech tissues, orchestrating complex alterations in host cellular architecture. These include both hyperplasia and hypertrophy of leaf cells, indicative of a finely tuned manipulation of the host's developmental and physiological pathways. This review synthesizes current research on the biology, ecology, and transmission dynamics of L. crenatae, with particular focus on its intricate interaction with beech tissues. By integrating recent findings across disciplines, this review aims to clarify the pathogenesis of L. crenatae as it causes BLD and identify critical knowledge gaps that must be addressed to inform the development of effective and sustainable management strategies for this emerging forest disease.
TALEs (transcription activator-like effectors) are an excellent example of how studying pathogen-host interactions can lead to significant biotechnology inventions. TALEs are bacterial effectors that are translocated into plant cells via a bacterial type III secretion system. Once inside the host cell, they are imported into the nucleus to bind specific promoters and induce expression of target genes, thereby supporting the bacterial infection. TALEs are found throughout many, but not all, Xanthomonas pathovars, which can be severe pathogens of different crops. The key feature of TALEs is their modular DNA-binding domain, which allows a simple evolutionary adaptation to novel DNA sequences as well as simple cloning of designer TALEs with desired DNA-binding specificity. Accordingly, TALE nucleases started the genome-editing revolution, and TALE base editors are the latest tools to efficiently edit chloroplast and mitochondrial genomes. We review recent advances in Xanthomonas genomics, synthesize current knowledge about naturally occurring TALEs, and highlight current roles of TALEs in genome editing and synthetic biology.
Vegetatively propagated crops such as cassava, potato, sweetpotato, and yam, or roots and tubers (RTs), play a major role in food security in low- and middle-income countries, yet phytosanitary issues in the tropics lead to substantial yield and quality losses. Challenges to production include institutional limitations that prevent effective responses and potential buildup of pathogens during clonal propagation. Addressing these challenges in a climate change context and diverse sociocultural environments requires a multifaceted approach, including improving access and availability to clean seed by strengthening seed systems; breeding for host resistance and disseminating resistant varieties; strengthening on-farm seed management; and designing effective policies and regulations to deal with seedborne diseases. Vital cross-cutting activities that can help to tackle the phytosanitary challenges of RTs include capacity strengthening, research on emergent pathogens, and improving regional cooperation and harmonization of phytosanitary standards to manage transboundary seed movement.
