Sara M. Villani

Reliable, up-to-date fungal and oomycete taxonomy underpins every aspect of plant pathology by enabling accurate pathogen identification, robust host-range analyses, clear assessment of geographic spread, and the development of effective disease management strategies. Yet, despite major advances in systematics and molecular phylogenetics, the integration and use of current names in applied plant pathology remains inconsistent. We discuss best practices for accurate identification, combining morphology, molecular data, and phylogenetic frameworks, and examine challenges arising from the use of informal or unofficial terms such as forma specialis. We outline formally recognized designations that can be used in lieu of forma specialis, such as the rank forma, which is governed by the International Code of Nomenclature for algae, fungi and plants and provides a more precise and reproducible means for describing variation below the species level. We use case studies of phytopathologically important fungi and oomycetes to illustrate recurring challenges, including misidentifications, species complexes, cryptic species, and pathogens with highly complex life cycles. We also provide practical guidance for nonexperts on how to navigate competing taxonomic concepts in their work. Finally, we outline a practical workflow for identifying plant pathogenic fungi and oomycetes to strengthen the link between taxonomy and plant pathology, incorporating curated databases, the deposition of voucher specimens, and collaboration between systematists and pathologists. In applied plant pathology, taxonomy and nomenclature are not merely academic concerns; researchers generate the correct identifications and reference data that diagnosticians, extension personnel, and industry translate into reliable diagnostics, fungicide efficacy and resistance management, regulatory information, and economically efficient disease management.

Boxwood blight, caused by the fungal pathogen Calonectria pseudonaviculata, has been reported in over 30 U.S. states and is a threat to boxwood production worldwide. Although considerable research has been conducted to evaluate the efficacy of conventional fungicides and cultural controls for this disease, the potential of host defense inducers remains largely unexplored. This study evaluated the effects of application method and frequency on managing boxwood blight in both container and field production systems in 2018 and 2019 at two locations in North Carolina. Actigard 50WG (acibenzolar- S-methyl) and LifeGard WG ( Bacillus mycoides isolate J) were applied as drench and foliar treatments to container-grown boxwoods artificially inoculated with C. pseudonaviculata and to field-grown boxwoods exposed to a natural inoculum. Drench applications of Actigard resulted in lower disease incidence than the untreated control plants under container production. High efficacy of Actigard was also observed under field production despite favorable environmental conditions for the development of boxwood blight. Application frequency did not affect disease for either of the tested host defense inducers in either production system. These findings support the integration of host defense inducers into cultural practice– and conventional fungicide–based management programs for boxwood blight.

Bacteriophages are viruses capable of infecting bacterial cells. Lytic phages, which infect and kill bacterial cells, are of interest in disease management in human, animal, and plant systems. In plant pathology, the biocontrol of bacterial diseases is of heightened interest because of the lack of efficacious options in many pathosystems. Numerous papers have been published in the past few decades on phage that target plant pathogenic bacteria, and a large majority of these have been focused on phage isolation and characteristics that highlight the promise and potential of phage as biocontrol agents. In contrast, relatively few of these papers have reported results from studies conducted in the field. Of the recent papers (2022 to 2025) reporting field studies, disease efficacy results are inconsistent. We argue that field studies should be an essential component of phage biocontrol research to understand how to best utilize and deploy phages to generate consistently effective disease management.

Rapid apple decline is a syndrome primarily affecting young (<6 yr old) apple trees planted in high-density orchards throughout the eastern United States and Canada. Despite the sudden death of thousands of apple trees in North America, no definitive biotic or abiotic cause of rapid apple decline has been identified. Surveys of apple orchards in North Carolina experiencing rapid apple decline symptoms in 2017 found that ambrosia beetle infestations were associated with dead or declining trees. The exotic ambrosia beetles (Coleoptera: Scolytinae), Xylosandrus crassiusculus (Motschulsky) and X. germanus (Blandford), have been implicated in damage and decline of ornamental, fruit, and nut trees throughout the United States and are of increasing concern in other regions throughout the world. Trapping surveys across western North Carolina apple orchards over 3 yr revealed that X. crassiusculus, X. germanus, and Xyleborinus saxesenii (Ratzeburg) were the dominant species captured, with annual variation in species composition. The same 3 species of beetles were found inside the scion, rootstock, and graft union of declining apple trees collected from commercial orchards. A large diversity of fungi was associated with beetle gallery and non-gallery tissue on declining trees, including opportunistic phytopathogenic genera such as Botryosphaeria, Fusarium, and Diaporthe. No phytopathogenic fungi appeared to be exclusively associated with gallery tissue. The establishment of several genera of opportunistic fungal pathogens and ambrosia beetles in rapidly declining apple trees suggests that rapid apple decline in North Carolina has no single cause and is likely due to a combination of abiotic and biotic stress events.

Glomerella leaf spot (GLS) and bitter rot caused by species in the Colletotrichum gloeosporioides species complex are the most economically devastating fungal diseases of apples in North Carolina. Crop losses have reached 100% in highly susceptible cultivars. In the southeastern United States, management of this disease has predominantly relied on broad-spectrum fungicide programs targeting several summer diseases of apples. To improve control of GLS and bitter rot, field experiments to evaluate the efficacy of multi- and single-site fungicides were conducted over multiple years in a ‘Gala’ research orchard in Mills River, NC, from 2017 to 2019. Fungicides representing different modes of action were applied in a nonrotational program from petal fall until the immediate preharvest period to assess their efficacy in reducing GLS incidence, shoot defoliation caused by GLS, and pre- and postharvest bitter rot. Of the fungicides evaluated, Captan 80WDG (active ingredient [a.i.] captan), Merivon (a.i. fluxapyroxad and pyraclostrobin), Cabrio (a.i. pyraclostrobin), and Aprovia (a.i. benzovindiflupyr) provided good to excellent control against disease caused by Colletotrichum chrysophilum. In these programs, the incidence of GLS, expressed as the relative area under the disease progress curve, ranged from 4.6 to 43.8 in the Captan 80WDG (2019) and the Aprovia (2017) programs, respectively. The incidence of bitter rot at harvest in these programs from 2017 to 2019 ranged from 0.0 to 45.3% in the 2018 and 2017 Captan 80WDG programs, respectively. Conversely, the highest incidences of GLS and preharvest bitter rot were consistently observed in the Inspire (a.i. difenoconazole), Sercadis (a.i. fluxapyroxad), and untreated programs. Shoot defoliation owing to GLS followed a similar trend across the evaluated fungicide programs. In addition to nonrotational fungicide programs, the effect of carrier water pH for applications of captan was evaluated for bitter rot control in Virginia and North Carolina. No differences in captan efficacy were observed at either location. The results of this study will inform the development of new management programs for GLS and bitter rot in the southeastern United States and provide a foundation for the development of new season-long fungicide programs for apple disease management.

Glomerella leaf spot (GLS), Glomerella fruit rot (GFR), and apple bitter rot (ABR), caused by Colletotrichum spp., are among the most devastating apple diseases in the southeastern United States. Although several species have been identified as causal pathogens of GLS, GFR, and ABR, their relative frequency and fungicide sensitivity status in the southeastern United States is unknown. In total, 381 Colletotrichum isolates were obtained from symptomatic leaves and fruit from 18 conventionally managed apple orchards and two baseline populations in western North Carolina and Georgia in 2016 and 2017. Multilocus DNA sequence analysis revealed that C. chrysophilum was the predominant cause of GLS and GFR and C. fioriniae was the causal agent of ABR. Baseline and commercial populations of Colletotrichum spp. were evaluated for sensitivity to pyraclostrobin and trifloxystrobin, and no statistical differences in sensitivity between the two species were observed for conidial germination. However, the effective concentration that inhibited growth by 50% values were significantly lower for C. fioriniae compared with C. chrysophilum for both fungicides regarding mycelial inhibition. Isolates recovered from commercial orchards revealed that five populations of C. chrysophilum and one population of C. fioriniae had reduced sensitivity to trifloxystrobin, and one C. fioriniae population had reduced sensitivity to pyraclostrobin via conidial germination assays. The cytb gene for 27 isolates of C. fioriniae, C. chrysophilum, and C. fructicola with different quinone outside inhibitor (QoI) sensitivities revealed the G143A mutation in a single isolate of C. chrysophilum with insensitivity to both fungicides. The results of these studies suggest that two Colletotrichum spp. predominantly cause GLS and ABR in the southeastern United States and that a reduction in sensitivity to some QoI fungicides may be responsible for control failures. This study also provides a basis for monitoring shifts in QoI sensitivity in Colletotrichum spp. causing disease on apple in the southeastern United States.

Fire blight, caused by the pathogen Erwinia amylovora, is a significant bacterial disease affecting pome fruit production globally. Symptoms include water soaking of floral tissue, blackening of leaf midribs, shoot wilt resembling a shepherd's crook, and at later stages may include lesions and wide-spread necrosis, potentially resulting in tree death. This report evaluates 11 different treatments consisting of individual or combined biorational and conventional treatments in addition to an untreated control group. The trial was conducted on 3-year-old Malus × domestica ‘Gala’ trees on G890 rootstock. Results from this trial provide will inform growers of potential antibiotic alternatives for the management of the blossom blight stage of fire blight disease in apple.

Marssonina leaf blotch (MLB) is a disease of apple caused by the fungal pathogen Marssonina coronaria. On foliage, MLB results in grayish-brown to purple leaf lesions, progressing into chlorosis and defoliation. This report evaluates the efficacy of both conventional and biological fungicides in controlling development of MLB symptoms. The trial was conducted at the Mountain Horticultural Crop Research and Extension Center in Mills River, NC, on 23-year-old Malus × domestica ‘Rome Beauty’ trees. Results from the trial will help advise growers in developing management programs for MLB, as well as provide insight into options for spray programs that utilize reduced loads of conventional fungicides.

Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field, as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work, we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected; however, relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage−pathogen dynamics is required to optimize disease control efficacy.