Short‐ and long‐read metabarcoding of Archaeorhizomycetes reveals high phylogenetic diversity structured by vegetation and climate

Archaeorhizomycetes is a class of globally widespread soil-dwelling fungi, originally proposed to be associated with plant roots, but their ecology and nutritional mode are not clearly defined. To increase the knowledge about Archaeorhizomycetes' ecology and biogeography, we investigate how they are distributed along major environmental gradients, as well as different soil compartments. To assess their abundance and diversity, we use both short- and long-read metabarcoding with class-specific primers for the long reads. The short-read sequences revealed that Archaeorhizomycetes is proportionally abundant and a dominant fungal class in alpine vegetation types, as well as boreal spruce and pine forests. The long-read sequences revealed high phylogenetic diversity of Archaeorhizomycetes, with 120 OTUs grouping into 13 clades with potentially differing ecologies and biogeographic distributions. Vegetation types and climate primarily structure the Archaeorhizomycetes community, while community composition was similar in litter, soil, and roots. However, Archaeorhizomycetes were significantly more abundant in soil and plant roots than litter, supporting the idea that Archaeorhizomycetes depend on the presence of plant roots. Our study illustrates that targeted group-specific amplification coupled with long-read sequencing is a powerful approach for exploring the diversity and ecology of specific fungal groups.