Annual Review of Phytopathology - Early Publication

Significant advances have been made in understanding mechanisms of plant defense against biotrophic and necrotrophic pathogens. Whole-genome sequencing of these pathogens has uncovered the genetic underpinnings of the distinct and common virulence and defense mechanisms. Necrotrophic pathogens produce toxins, necrosis-inducing proteins, secondary metabolites, and hydrolytic enzymes, and their virulence generates endogenous plant peptides. The recognition of these factors triggers broad-spectrum quantitative resistance. Resistance to specialist, host-specific, toxin-producing pathogens is mediated by the absence of host susceptibility proteins, including nucleotide-binding leucine-rich repeats (NLRs), or by detoxification mechanisms. Biotrophic pathogens utilize distinct virulence strategies, and NLR proteins are critical determinants of resistance, interacting synergistically with other quantitative resistance factors. However, NLRs are ineffective against necrotrophs, which exploit canonical immune responses to establish and promote disease. Immune responses such as hypersensitive cell death and the production of reactive oxygen species and accumulation of hormones exhibit distinct or complex roles in defense against biotrophic and necrotrophic pathogens. Lately, the microbiome has become instrumental in uncovering novel pathogen resistance mechanisms. However, further studies are needed to understand the genes involved in recruiting defense-promoting microbes and their impact on pathogens with distinct virulence. Overall, a comprehensive understanding of mechanisms of resistance to biotrophic and necrotrophic pathogens is crucial for activating or suppressing appropriate host responses.

Phytopathogenic and food spoilage microorganisms are major contributors to postharvest crop losses. Some species of fungi are able to produce mycotoxins, posing health risks to both humans and animals. Control methods based on synthetic fungicides raised environmental and health concerns and led to the development of fungicide-resistant pathogens. As a result, biological control has gained momentum as an eco-friendly alternative. Microbial biocontrol agents (BCAs) are increasingly being commercialized, with recent research exploring volatile-mediated interactions between BCAs, pathogens, and the treated commodities. Volatile organic compounds (VOCs) play a crucial role in biocontrol. This review focuses on fungal volatiles, their chemical diversity, their effects, and the application of VOC-emitting fungi or synthetic VOCs as biofumigants. Future research directions include enhancing VOC-producing agents through targeted mutagenesis and synthetic biology, understanding interspecies interactions, and applications of artificial intelligence in analytical chemistry, which shall lead to increased efficiency and precision in postharvest biocontrol.

Plant susceptibility (S) genes exploited by pathogenic bacteria play critical roles in disease development, collectively contributing to symptoms, pathogen proliferation, and spread. S genes may support pathogen establishment within the host, suppress host immunity, regulate host physiology or development, or function in other ways. S genes can be passive, e.g., involved in pathogen attraction or required for pathogen effector localization or activity, or active, contributing directly to symptoms or pathogen proliferation. Knowledge of S genes is important for understanding disease and other aspects of plant biology. It is also useful for disease management, as nonfunctional alleles can slow or prevent disease and, because they are often quantitative, can exert less selection on pathogens than dominant resistance genes, allowing greater durability. In this review, we discuss bacterial exploitation of S genes, S-gene functional diversity, approaches for identifying S genes, translation of S-gene knowledge for disease control, and future perspectives on this exciting area of plant pathology.

The chestnut blight pathogen Cryphonectria parasitica is well-known for the devastation it caused to North American forests. It is less well recognized that numerous other fungi in the Cryphonectriaceae are emerging as threats to native and planted forests in the tropics and Southern Hemisphere. Unlike C. parasitica, these fungi, such as Chrysoporthe cubensis, initially gained attention due to a canker disease in plantations of non-native Eucalyptus. More than four decades of research have revealed a wide diversity of Cryphonectriaceae species that infect many other tree genera in the Myrtales. These fungi often exist as endophytes but become problematic when trees are planted outside their native range. Growing numbers of species are also undergoing host shifts from native to susceptible trees such as Eucalyptus, posing serious risks to both natural and planted forests. These fungi provide an example of the biodiversity of tree-infecting fungi that is understudied, despite their significant potential to harm forest ecosystems.

As obligate intracellular parasites, viruses depend entirely on host cells for propagation, with replication being the central process in establishing their infections. Upon entry into host cells, positive-strand RNA viruses induce rearrangement of the host's cellular membranes, leading to the formation of virus replication organelles (ROs). Advancements in imaging techniques have enabled the determination of three-dimensional structures for several plant viral ROs that are associated with specific organelle membranes and display either spherule- or tube-shaped structures. Viral replication proteins, along with diversely recruited host factors such as lipids and membrane-shaping proteins, are used to remodel cellular membranes and build ROs. These ROs not only shield viral replication templates and intermediates from host defense mechanisms but also serve as efficient machinery for the synthesis of viral RNAs. Moreover, ROs are intricately connected to other stages of the viral life cycle, often triggering stress responses and redox shifts within the cellular microenvironment, positioning the ROs as central hubs for virus–plant interactions.

The success of plant-parasitic nematodes (PPNs) depends on the integration of sensory cues and neuromuscular motor outputs, leading to behaviors such as hatching, host-finding, locomotion, feeding, and reproduction. Although the nervous system is often a target for control, much of our knowledge of PPN nervous system structure and function has been inferred from the free-living nematode Caenorhabditis elegans. However, the past two decades have seen substantial advances in our understanding of PPN nervous systems. These suggest that although many features of PPN neurobiology are conserved across nematodes, the behavioral repertoire of PPNs also requires distinct neuronal, structural, and functional properties that have diverged from their free-living ancestors. This review focuses on host-finding and feeding behaviors and their underlying neuronal basis; however, the diversity of PPNs implies there is much to be discovered in the rich repertoire of PPN behaviors.

Wheat yields have continued to increase globally at a steady pace over the past decade despite challenges faced by breeding programs from evolving and migrating races of rust and other wheat disease–inducing fungi. Additionally, pathogens are becoming tolerant to fungicides because of their injudicious use. We highlight the challenges in breeding and deploying resistant varieties and discuss global strategies to protect wheat from diseases. The continuous identification, utilization, and deployment of diverse resistance genes and quantitative trait loci for durable adult plant resistance, supported by precision phenotyping, marker-assisted and genomic selection, real-time pathogen diagnostics, and the rapid diffusion of resistant varieties, are helping to minimize crop losses while enhancing productivity. The potential for genetic engineering, including the introduction of resistance gene cassettes and precise genome editing of susceptibility or resistance genes, has also increased because of the recent acceptance of genetically modified wheat carrying the HB4^® drought tolerance gene in some countries.

To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.