First Report of Cobweb Disease in Oudemansiella raphanipes Caused by Cladobotryum varium in Beijing, China

Oudemansiella raphanipes is an edible mushroom with medicinal properties,which has been recently cultivated throughout China (Hao et al. 2016). In October 2019, a disease with symptoms similar to that of cobweb disease (Carrasco et al. 2017) was observed in O. raphanipes in the Tongzhou District, Beijing, China, infecting 25% of the fruiting bodies (Fig. 1A, B). White cotton-like net of hyphae were present typically on the casing soil or on the stipe of the fruiting bodies; they gradually spread to the pileus, covering the fruiting body, which eventually wilted and died (Fig. 1C, D), resulting in yield reduction and economic loss. Cultures were obtained by aseptically transferring the diseased fruiting bodies onto potato dextrose agar (PDA) at 25 °C; they were deposited in the culture collection (ID: JZBQA1) of the Beijing Academy of Agricultural and Forestry Sciences, China. The colonies were pale white/white, with an occasional formation of yellow diffusing pigments on the reverse side (Fig. 1E–G). Conidiophores were Cladobotryum-like, phialides were solitary or commonly divergent in whorls of 2–3 (–4), lageniform to subulate, 20–63.5 (–66) × (3.8–) 4–5.3 (–9) μm (n = 40) (Fig. 1H, I); conidia were hyaline, oval to ellipsoidal, with one or two septa, (10.4–) 11.4–20 (–22) × 6.6–9.5 (–10) μm (n = 40) (Fig. 1J); chlamydospores were globose or ellipsoidal (Fig. 1K). The morphological characteristics were consistent with that of Cladobotryum varium (Back et al. 2012a, b; Sun et al. 2019). For species-level fungal identification, genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen, USA). The internal transcribed spacer (ITS) regions, translation elongation factor 1 alpha exon (TEF1-α), RNA polymerase II subunit b (RPB2), and RNA polymerase I largest subunit (RPB1) genes were amplified using the primer pairs ITS1/ITS4 (White et al. 1990), EF1-983F/2218R (Rehner and Buckley 2005), RPB2-5F/7cR (Liu et al. 1999), and RPB1F1 (5'-GCCGATGAAGTTGGTCTA-3')/RPB1R1 (5'-TATGTTGCGGTGAGCCTT-3'), respectively. A BLAST nucleotide search showed 99.34% (449/452 bp), 99.24% (914/921 bp), 98.08% (1,022/1,042 bp), and 99.66% (588/590 bp) homology, respectively, with those of the ex-type culture of Hypomyces aurantius TFC 95-171 (FN859425.1, FN868743.1, FN868679.1, and FN868805.1). The four sequences were deposited in GenBank (accession numbers: MW534093, MW560066, MW560064, and MW560065). Phylogenetic trees based on the assessed gene loci revealed that the JZBQA1 strain was closely related to C. varium (Fig. 2). A in vivo pathogenicity test was performed using the fruiting bodies (Fig. 1L, O). Spore suspension (108 spores/mL) of the JZBQA1 strain or sterile distilled water was sprayed on six healthy fruiting bodies, maintained in an artificial climate chamber at 24-26°C. Cobweb-like features were observed on the fruiting bodies treated with the spore suspension 2-3 days post-inoculation; while those treated with water did not exhibit such features (Fig. 1L, O). The same pathogen was re-isolated and confirmed from the infected fruiting bodies by integrated analysis of morphological characteristics and gene sequencing data. Cladobotryum spp. infects different varieties of cultivated edible mushrooms, resulting in the development of cobweb diseases (Cao et al. 2020; Carrasco et al. 2017). Cladobotryum varium is the causal agent of cobweb disease in Flammulina velutipes and Hypsizygus marmoreus (Back et al. 2012a, b). To our knowledge, this is the first report of cobweb disease caused by C. varium in O. raphanipes. This finding is a valuable contribution to the knowledge of cobweb disease development in edible fungi.

Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism

Cladobotryum dendroides, which causes cobweb disease in edible mushrooms, is one of the major fungal pathogens. Our previous studies focused on the genetic and morphological characterization of this fungus, as well as its pathogenicity and the identification of appropriate fungicides. However, little is known about the genome characters, pathogenic genes, and molecular pathogenic mechanisms of C. dendroides. Herein, we reported a high-quality de novo genomic sequence of C. dendroides and compared it with closely-related fungi. The assembled C. dendroides genome was 36.69 Mb, consisting of eight contigs, with an N50 of 4.76 Mb. This genome was similar in size to that of C. protrusum, and shared highly conserved syntenic blocks and a few inversions with C. protrusum. Phylogenetic analysis revealed that, within the Hypocreaceae, Cladobotryum was closer to Mycogone than to Trichoderma, which is consistent with phenotypic evidence. A significant number of the predicted expanded gene families were strongly associated with pathogenicity, virulence, and adaptation. Our findings will be instrumental for the understanding of fungi–fungi interactions, and for exploring efficient management strategies to control cobweb disease.

Screening and Evaluation of Essential Oils from Mediterranean Aromatic Plants against the Mushroom Cobweb Disease, Cladobotryum mycophilum

The main aim of this study was to evaluate the use of essential oils (EOs) as an alternative to synthetic fungicides used in the control of cobweb disease of button mushroom (Agaricus bisporus) caused by Cladobotryum mycophilum. The EOs used were obtained by hydrodistillation from five Mediterranean aromatic species (Lavandula × intermedia, Salvia lavandulifolia, Satureja montana, Thymus mastichina, and Thymus vulgaris), analyzed by gas chromatography, and tested in vitro for their antifungal activity against C. mycophilum. In vitro bioassays showed that the EOs obtained from T. vulgaris and S. montana (ED50 = 35.5 and 42.8 mg L−1, respectively) were the most effective EOs for inhibiting the mycelial growth of C. mycophilum, and were also the most selective EOs between C. mycophilum and A. bisporus. The in vivo efficacy of T. vulgaris and S. montana EOs at two different concentrations (0.5 and 1%) were evaluated in two mushroom growing trials with C. mycophilum inoculation. The treatments involving T. vulgaris and S. montana EOs at the higher dose (1% concentration) were as effective as fungicide treatment. The effect of these EOs on mushroom productivity was tested in a mushroom cropping trial without inoculation. They had a strong fungitoxic effect at the first flush. However, a compensatory effect was observed by the end of the crop cycle and no differences were observed in biological efficiency between treatments. The main compounds found were carvacrol and p-cymene for S. montana, and p-cymene and thymol for T. vulgaris. These results suggest that T. vulgaris and S. montana EOs may be useful products to manage cobweb disease if used as part of an integrated pest management (IPM) program.

Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen–host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.

Identification of resistance to cobweb disease caused byCladobotryum mycophilumin wild and cultivated strains ofAgaricus bisporusand screening for bioactive botanicals

Outbreaks of cobweb disease are becoming increasingly prevalent globally, severely affecting the quality and yield ofAgaricus bisporus.