*3.2. Composition of Fungal Microbiomes in MOR and AOF Samples*

In the MOR group, the dominant phylum was Ascomycota with a relative abundance of 49.53–94.32%, whereas the other phyla were low in abundance (Figure 2a). Eurotiomycetes, Dothideomycetes, and Sordariomycetes were dominant at the class level, accounting for 2.09–78.91%, 1.88–57.02%, and 0.60–20.37% of the fungal reads, respectively (Figure 2b). At the order level, Capnodiales was predominant in MCK1, GDM3, GXM1, GXM2, and GXM3, whereas Eurotiales was predominant in MCK2, MCK3, GDM1, and GDM2 (Figure 2c). Further taxonomical classification demonstrated that Aspergillaceae (1.90–76.73%) was the most dominant at the family level, followed by Cladosporiaceae (1.83–56.78%) and Trichocomaceae (0.12–20.45%, Figure 2d). At the genus level, *Penicillium* (1.86–76.14%), *Cladosporium* (1.82–56.65%), *Trichoderma* (0.12–19.71%), *Monascus* (0.00–19.35%), and *Talaromyces* (0.18–19.71%) were the top 5 genera with the highest relative abundance (Figure 3a). The top 20 abundant genera were visualized using a heatmap, which showed the relative abundance of fungal genera in different samples (Figure 3b).

In the AOF group, Ascomycota was the most abundant phylum representing 14.81–81.85%, followed by Basidiomycota (0.36–52.57%, Figure 4a). At the class level, Eurotiomycetes (0.57–56.84%), Tremellomycetes (0.11–51.81%), and Dothideomycetes (3.13– 46.37%) were prevalent (Figure 4b). Among the 39 orders detected, Eurotiales, Tremellales, and Capnodiales were dominant with the relative abundances of 0.41–56.29%, 0.09–51.78%, and 3.11–46.30%, respectively (Figure 4c). At the family level, the dominant fungi in samples ACK1 and HNA3 were Aspergillaceae (56.17%) and Rhynchogastremataceae (51.71%), respectively. Cladosporiaceae was dominant in the rest of the samples representing 5.71– 46.30% (Figure 4d). *Penicillium* (0.27–56.06%), *Papiliotrema* (0.04–51.71%), and *Cladosporium* (3.08–44.41%) were dominant at the genus level (Figure 5a). *Candida* was the subdominant genus in the ACK1 with the relative abundance of 11.95%, while it accounted for low levels in other samples (0.00–4.51%). A heatmap of the 20 most abundant genera is presented in Figure 5b.

**Figure 2.** Fungal composition of the MOR samples at the phylum (**a**), class (**b**), order (**c**), and family (**d**) levels.

**Figure 3.** Composition analyses of the fungal microbiomes in the MOR samples. (**a**) Fungal composition in MOR samples at genus level; (**b**) Heatmap of the top 20 genera in MOR samples.

**Figure 4.** Fungal composition of the AOF samples at the phylum (**a**), class (**b**), order (**c**), and family (**d**) levels.

**Figure 5.** Composition analyses of the fungal microbiomes in the AOF samples. (**a**) Fungal composition in AOF samples at genus level; (**b**) Heatmap of the top 20 genera in AOF samples.

It is worth noting that a potential toxigenic fungus, namely, *Trichoderma atroviride*, was detected in all samples. Furthermore, another potential toxigenic fungus (*Fusarium equiseti*) was detected in four non-moldy samples (MCK1, MCK2, ACK1, and ACK3). The species and relative abundance of harmful fungi in each sample are shown in Supplementary Table S2.
