| Summary: | The rhizosphere fungal community is essential for determining plant health and improving crop productivity. The fungal community structure and functional roles in the plastic shed soils were explored using high throughput sequencing and FUNGuild in this study. The fungal community structures shifted between the rhizosphere and non-rhizosphere soils. The greatest abundance variation was observed for the rare fungal members with relative abundances <0.1%. In the rhizosphere soil of pepper, the abundance of the genera <i>Purpureocillium</i>, <i>Metacorgyceps</i>, <i>Arthrobotrys</i>, <i>Cephalotheca</i>, and <i>Scedosporium</i> increased significantly, among which, <i>Purpureocillium</i>, <i>Arthrobotrys</i> and <i>Metacorgyceps</i> exhibited biocontrol characteristics. Co-occurrence network analysis revealed different interactions of fungal communities in the rhizosphere and non-rhizosphere soils, both of which were dominated by low abundance members. More positive correlation was identified among the rare members, the fungal pathotroph functions and phthalate acid ester in the rhizosphere soil. This study highlights the important niche of the rare fungal members in soil microbial ecology under plastic shed cultivation.
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