Apple is an economically important fruit crop in northern Shaanxi Province in China. In recent years, a new type of apple black spot disease, “bagged apple black spot disease,” has occurred in the main apple production area of Yan’an City, Shaanxi Province, during the apple ripening season. It seriously affects the appearance quality and commercial value of apples. In this study, 120 isolates recovered from symptomatic apples were identified based on morphological characteristics, pathogenicity, and multilocus sequence analyses of the internal transcribed spacer of ribosomal DNA (rDNA-ITS), translation elongation factor 1-α (EF1-α), RNA polymerase II subunit B (RPB2), endopolygalacturonase (endo-PG), and anonymous region OPA1-3. Alternaria alternata was the most abundant species (64%), followed by Fusarium acuminatum (36%). Pathogenicity assays were conducted by inoculating them individually and together on detached apples (Venus Golden and Fuji varieties). The results showed that the two fungal species could infect apples individually and together. Co-infection enhanced the disease severity. F. acuminatum led to increased severity and speed of disease development compared to A. alternata. This is the first report of Fusarium and Alternaria co-infection causing apple black spot disease worldwide, and the first report of F. acuminatum affecting apples. The optimal growth of A. alternata occurred at 25–30°C and pH 7; the optimal growth of F. acuminatum occurred at 25°C and pH 7. The results of this study can provide a theoretical basis for exploring the occurrence and epidemiology of apple black spot disease and strategies for its control.

Plant fungal diseases remain a major threat to global agricultural production, necessitating eco-friendly and sustainable strategies. Conventional chemical fungicides often lead to the development of resistant pathogen strains and cause environmental contamination. Therefore, the development of biocontrol agents is particularly important. In this study, we identified Burkholderia stagnalis YJ-2 from the rhizosphere soil of Woodsia ilvensis as a promising biocontrol strain using 16S rRNA and whole-genome sequencing. This strain demonstrated broad-spectrum antifungal activity against plant fungal pathogens, with its bioactive extracts maintaining high stability across a temperature range of 25–100 °C and pH range of 2–12. We used in vitro assays to further show that the metabolites of B. stagnalis YJ-2 disrupted the hyphal morphology of Valsa mali, resulting in swelling, reduced branching, and increased pigmentation. Fluorescence labeling confirmed that B. stagnalis YJ-2 stably colonized the roots and stems of tomato and wheat plants. Furthermore, various formulations of microbial agents based on B. stagnalis YJ-2 were evaluated for their efficacy against plant pathogens. The seed-coating formulation notably protected tomato seedlings from Alternaria solani infection without affecting germination (p > 0.1), while the wettable powder exhibited significant control effects on early blight in tomatoes, with the preventive treatment showing better efficacy than the therapeutic treatment. Additionally, the B. stagnalis YJ-2 bone glue agent showed a substantial inhibitory effect on apple tree canker. Whole-genome analysis of B. stagnalis YJ-2 revealed a 7,705,355 bp genome (67.68% GC content) with 6858 coding genes and 20 secondary metabolite clusters, including three clusters (YJ-2_GM002015-YJ-2_GM002048, YJ-2_GM0020090-YJ-2_GM002133, and YJ-2_GM06534-YJ-2_GM006569) that are related to the antifungal activity of YJ-2 and are homologous to the biosynthetic gene clusters of known secondary metabolites, such as icosalide, ornibactin, and sinapigladioside. We further knocked out core biosynthetic genes of two secondary metabolic gene clusters and found that only the YJ-2_GM006534-YJ-2_GM006569 gene cluster had a corresponding function in two potential antifungal gene clusters. In contrast to the wild-type strain YJ-2, only deletion of the YJ-2_GM006563 gene reduced the antifungal activity of B. stagnalis YJ-2 by 8.79%. These findings highlight the biocontrol potential of B. stagnalis YJ-2, supporting a theoretical foundation for its development as a biocontrol agent against plant fungal diseases and thereby promoting sustainable agricultural disease management.

Hyjpsizygus marmoreus (Peck) H.E. Bigelow is one of the most popular and widely cultivated edible mushrooms worldwide. In June 2021, an epidemic of H. marmoreus fruiting bodies infected with brown rot occurred at a cultivation facility in Yan’an (Shaanxi province), China, which resulted in a 90% economic loss. The fruiting body surface was covered with white-to-gray velvet-like mycelia, which gradually spread to the pileus, eventually covering the whole fruiting body (Fig. 1A). Brown rot, which is the most important factor limiting H. marmoreus fruiting body yield and quality, is responsible for severe economic losses in northern Shaanxi province. To identify the causal agent of this disease, small pieces of diseased tissue were collected from fruiting bodies, disinfected with 70% ethanol, and rinsed three times with sterile distilled water. They were then placed on potato dextrose agar (PDA) medium in plates and incubated at 26 °C. The colonies on the PDA medium after a 14-day incubation at 26 °C were 40–45 mm in diameter, orange–white on the surface (Fig. 1B), pale orange on the underside (Fig. 1C), slightly wrinkled or cerebriform, and glabrous or fasciculate. Vegetative hyphae were septate, hyaline, smooth, and thin-walled. The unicellular conidia were cylindrical with rounded ends (3.5 to 4.0 × 1.0 to 1.5 μm; n = 30). The cultural and morphological characteristics of the representative isolate MG1 were consistent with those of Sarocladium kiliense (Grütz) Summerbell (Giraldo et al. 2015). For the molecular identification, DNA was extracted from MG1. The internal transcribed spacer (ITS) region, a gene encoding the second largest RNA polymerase II subunit (RPB2), a β-tubulin gene (TUB2), and an actin gene (ACT) were amplified by PCR using primers ITS1/ITS4, fRPB2-5F/fRPB2-7cR, Bt2a/Bt2b, and ACT-512F/ACT-783R, respectively. The resulting ITS (MZ818340), RPB2 (MZ833454), TUB2 (MZ833455), and ACT (MZ833456) sequences from MG1 were 99.82%, 99.19%, 99.69%, and 99.22% identical to the corresponding sequences in S. kiliense isolate CBS 400.52 (ITS: KM231849, RPB2: KM232425, TUB2: KC479789, and ACT1: KM231258). On the basis of the morphological and molecular features, MG1 was identified as S. kiliense (Summerbell et al. 2011; Lombard et al. 2015; Giraldo et al. 2015). Pathogenicity tests, which were repeated three times, were conducted using conidial suspensions (approximately 1 × 105 spores/mL) prepared in sterile distilled water. The surface of 30 healthy H. marmoreus fruiting bodies maintained in a plastic box was sprayed with the MG1 conidial suspensions. Control H. marmoreus fruiting bodies were sprayed with sterile distilled water. The inoculated fruiting bodies were maintained in darkness at 25 °C and 95% relative humidity. The disease symptoms that developed in 3 days included the presence of gray mycelia on the fruiting body surface. Additionally, S. kiliense was reisolated from symptomatic pilei at 6 days post-inoculation. Disease symptoms were undetectable on the negative control. To the best of our knowledge, this is the first report of H. marmoreus infected with brown rot caused by S. kiliense in China.

Stone and pome fruit trees play a significant role in fruit production and consumption in China. As an economic fruit tree variety in Shaanxi Province, the cultivation area of Malus ‘Jinxiu’ has been gradually expanding. Brown rot, caused by several species of the genus Monilinia, can result in flower blight and fruit rot, leading to serious economic losses. In September 2025, brown rot symptoms were observed on Malus ‘Jinxiu’ fruits in orchards in Shaanxi Province, China. A total of 90 isolates recovered from symptomatic fruits were identified based on morphological characteristics, pathogenicity, and multi-locus sequence analyses of the internal transcribed spacer of ribosomal DNA (rDNA-ITS), β-tubulin gene (tub2), and laccase genes (lcc2). The results showed that the causal agent of Malus ‘Jinxiu’ brown rot in Shaanxi Province is Monilinia yunnanensis. Furthermore, upon artificial inoculation, M. yunnanensis isolates from both Malus ‘Jinxiu’ and ‘Fuji’ apple hosts can cross-infect and cause brown rot symptoms. At the same time, a M. yunnanensis isolate from Malus ‘Jinxiu’ showed similar virulence on five other local cultivated apple varieties. To our knowledge, this is the first report of M. yunnanensis infecting Malus ‘Jinxiu’. This study provides a basis for developing field diagnosis and integrated control measures for brown rot disease of Malus ‘Jinxiu’ in Shaanxi Province, China.