Mee-Sook Kim

In this study, we used coniferous and non-coniferous hosts to assess the pathogenicity of a Fusarium annulatum isolate derived from southwestern white pine ( Pinus strobiformis), along with F. commune isolates derived from coniferous and herbaceous, non-conifer hosts. All isolates of both Fusarium spp. were found to be pathogenic to conifer hosts. For the tested non-coniferous hosts, F. commune isolates were found to be pathogenic to both rice and tomato, whereas F. annulatum was pathogenic to rice and potentially less aggressive on tomato. To investigate the molecular basis of pathogenicity, we identified differentially expressed pathogenicity-/virulence-associated genes by inoculating loblolly pine ( P. taeda) seedlings with isolates of conifer-derived F. commune (collected from ponderosa pine [ P. ponderosa]) and F. annulatum (collected from southwestern white pine), which were all previously confirmed to be pathogenic to loblolly pine in our assays. Seedlings were harvested at 12, 24, and 48 h postinoculation for transcriptomic analyses to identify pathogen genes associated with early infection of the host. Among the upregulated in planta (UIP) genes, we identified putative pathogenicity-/virulence-associated genes, including secreted effectors, secondary metabolite gene clusters involved in mycotoxin biosynthesis, and carbohydrate-active enzymes. To identify the putative conifer pathogenicity profiles of these potential conifer pathogens, we compared these UIP genes with the predicted proteomes of 17 conifer-associated Fusarium spp. isolates. These putative pathogenicity profiles did not definitively correspond with pathogenicity on coniferous versus herbaceous hosts but rather aligned with Fusarium species complexes. A subset of these shared UIP genes may aid in the development of detection methods for conifer-specific pathogens based on Fusarium species complexes. [ ] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

The genus Armillaria is a broad group of basidiomycete (Agaricales, Physalacriaceae) plant pathogens that can have detrimental effects on woody hosts in forested, urban, and horticultural landscapes. Several species are known as aggressive root pathogens on both conifers and deciduous woody plants. Armillaria species are considered white rot fungi due to their capacity to degrade both lignin and cellulose in woody tissues. Armillaria mexicana was recently described as a new species found in peach (Prunus persica) orchards of Coatepec Harinas, State of Mexico. However, a subsequent study identified A. mexicana on avocado (Persea americana) and pine (Pinus sp.), suggesting that A. mexicana may be able to infect diverse hosts that are planted in disturbed areas following deforestation. We assembled a reference genome for A. mexicana consisting of 38 contigs constructed using PacBio and Illumina sequencing reads. Genome annotation and comparison with A. mellea, a phylogenetic sister taxon, revealed notable differences, including a larger number of interspersed repeats in A. mexicana and the absence of small RNAs, which were detected in A. mellea. While A. mexicana (49 Mb) has a roughly 30% smaller genome than A. mellea (70 Mb), it has a similar number of genes encoding pectinases and nonribosomal peptide synthetase (NRPS) and NPRS-like secondary metabolites, which may influence the pathogenicity of A. mexicana. This reference genome of A. mexicana allows future genomic comparisons that can help characterize the evolutionary history and enhance our understanding of the molecular mechanisms involved in pathogenicity and wood decomposition of Armillaria species.

Although Armillaria solidipes was described in 1900, confusion has surrounded the appropriate use of this taxonomic epithet, largely because DNA sequence-based characterization and an associated culture were unavailable for the original holotype. An epitype for A. solidipes (previously known as North American Biological Species I) is established herein, along with morphological descriptions and genetic characterization that clearly distinguish A. solidipes, which is found in North America, from A. ostoyae (previously known as European Biological Species C), which is found in Eurasia. Of the five loci examined, translation elongation factor 1-alpha was the most useful for distinguishing A. solidipes from other Armillaria spp. including A. ostoyae. Further, the whole genome phylogeny of A. solidipes and A. ostoyae showed substantial differences that further demonstrate their separation. The specimen from Colorado, USA, which was collected in the locality where the original type specimen was collected, is designated as the epitype.

Korean oak wilt disease associated with Dryadomyces quercus-mongolicae recently emerged as a major tree disease in South Korea. A comprehensive transcriptome analysis is presented for D. quercus-mongolicae grown in vitro on three different culture media, identifying nearly 7,000 expressed transcripts. Most transcripts are associated with proteins essential for fungal survival and growth. The 40S ribosomal protein S25, ceramide very long chain fatty acid hydroxylase, Epl1 protein, and ADP/ATP translocase are particularly important due to their critical roles in the metabolism and environmental adaptation of fungi. Gene ontology analyses revealed that 39.4%, 61.2%, and 43.3% of transcripts were successfully annotated to biological process, molecular functions, and cellular component aspects, respectively. Furthermore, key metabolic pathways were elucidated, including sphingolipid metabolism, L-tryptophan biosynthesis, and glycolysis, which provide important information on physiological functioning of D. quercus-mongolicae. Overall, these findings provide key information on fundamental biological mechanisms of D. quercus-mongolicae.

Fires in coniferous forests throughout the northern United States alter ecosystem processes and ecological communities, including the diversity and composition of microbial communities living in the soil. In addition to its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. Altering the microbiome composition to promote taxa that inhibit pathogenic activity has been suggested as a management strategy for forest diseases, including Armillaria root disease caused by Armillaria solidipes , which causes growth loss and mortality of conifers. These forest ecosystems are experiencing increased wildfire burn severity that could influence A. solidipes activity and interactions of the soil microbiome with Armillaria root disease. In this research, we examine changes to the soil microbiome following three levels of burn severity in a coniferous forest in northern Idaho, United States, where Armillaria root disease is prevalent. We further determine how these changes correspond to the soil microbiomes associated with the pathogen A. solidipes, and a putatively beneficial species, A. altimontana . At 15-months post-fire, we found significant differences in richness and diversity between bacterial communities associated with unburned and burned areas, yet no significant changes to these metrics were found in fungal communities following fire. However, both bacterial and fungal communities showed compositional changes associated with burn severity, including microbial taxa with altered relative abundance. Further, significant differences in the relative abundance of certain microbial taxa in communities associated with the three burn severity levels overlapped with taxa associated with various Armillaria spp. Following severe burn, we observed a decreased relative abundance of beneficial ectomycorrhizal fungi associated with the microbial communities of A. altimontana, which may contribute to the antagonistic activity of this soil microbial community. Additionally, A. solidipes and associated microbial taxa were found to dominate following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Overall, our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in similar conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease. IMPORTANCE: With its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. These forest ecosystems are experiencing increased wildfire frequency and burn severity that could influence the fungal root pathogen, Armillaria solidipes , and interactions with the soil microbiome. We examined changes to the soil microbiome following three levels of burn severity, and examined how these changes correspond with A. solidipes , and a putatively beneficial species, A. altimontana . Following severe burn, there was a decreased relative abundance of ectomycorrhizal fungi associated A. altimontana . A. solidipes and associated microbial taxa dominated following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

Brown root rot disease (BRRD) is a highly destructive tree disease. Early diagnosis of BRRD has been challenging because the first symptoms and signs are often observed after extensive tissue colonization. Existing molecular detection methods, all based on the internal transcribed spacer (ITS) region, were developed without testing against global Phellinus noxius isolates, other wood-decay fungi, or host plant tissues. This study aimed to develop SYBR Green real-time quantitative PCR (qPCR) assays for P. noxius. The primer pair Pn_ITS_F/Pn_ITS_R targets the ITS, and the primer pair Pn_NLR_F/Pn_NLR_R targets a P. noxius–unique group of homologous genes identified through a comparative genomics analysis. The homologous genes belong to the nucleotide-binding-oligomerization-domain-like receptor (NLR) superfamily. The new primer pairs and a previous primer pair G1F/G1R were optimized for qPCR conditions and tested for specificity using 61 global P. noxius isolates, 5 other Phellinus species, and 22 non-Phellinus wood-decay fungal species. Although all three primer pairs could detect as little as 100 fg (approximately 2.99 copies) of P. noxius genomic DNA, G1F/G1R had the highest specificity and Pn_NLR_F/Pn_NLR_R had the highest efficiency. To avoid false positives, the cutoff quantification cycle values were determined as 34 for G1F/G1R, 29 for Pn_ITS_F/Pn_ITS_R, and 32 for Pn_NLR_F/Pn_NLR_R. We further validated these qPCR assays using Ficus benjamina seedlings artificially inoculated with P. noxius, six tree species naturally infected by P. noxius, rhizosphere soil, and bulk soil. The newly developed qPCR assays provide sensitive detection and quantification of P. noxius, which is useful for long-term monitoring of BRRD status.

Recent studies have shown numerous Fusarium spp. are associated with symptomatic conifer seedlings in both bareroot and container nursery systems. Some of these species have been found pathogenic to conifer seedlings (e.g., F. avenaceum, F. commune, F. oxysporum, F. solani, and F. verticillioides), but the mechanisms and shared evolutionary history of these conifer pathogenic species have not been well studied in these pathosystems. We compared whole genomes of 17 Fusarium spp. associated with conifer seedlings to elucidate putative shared pathogenicity/virulence gene profiles presumably expressed for roles in causing damping‐off and/or root disease of conifer seedlings. In addition, this work provides draft genomes of conifer‐associated Fusarium spp. and genomes not previously referenced in public databases (e.g., F. lactis, F. fredkrugeri, F. ipomoeae, and F. flocciferum). We identified pathogenicity/virulence genes associated with Fusarium spp. pathogens of conifers including effectors, the secreted in xylem (SIX) genes 2, 4, 9 and 14 and secondary metabolites, and the mycotoxins fumonisin and deoxynivalenol. We conclude that gene profiles are shared within Fusarium species complexes and among closely related Fusarium species complexes; however, these shared profiles are widely distributed across all Fusarium pathogens. These findings highlight potential targets for detecting and/or identifying Fusarium pathogens of conifers, but multiple methods and/or targets will be required depending on the species complexes and clades. More research is needed to determine the roles of expressed pathogenicity/virulence genes and the downstream metabolic products that result in pathogenesis to conifers.