Peeking into the black box – integrated taxonomy of Archaeorhizomycetes

Due to their submerged and cryptic lifestyle the vast majority of fungal species are difficult to observe and describe morphologically and many remains known to science only from sequences detected in environmental samples. The lack of rules to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here we use environmental sequence data as taxonomical evidence and take an integrated taxonomic approach by combining phylogenetic and ecological data to generate and test species hypothesis in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing we recognize 68 distinct phylogenetic species hypotheses (PSHs) of Archaeorhizomycetes, including the two described species in the class, in a well-studied Swedish pine forest podzol soil. Nine of the species hypotheses, including the more abundant ones, are supported by long read data and represent 78% of the sequenced Archaeorhizomycetes community. Among well supported sister PSHs, significantly differential distribution in the soil profile provide additional ecological evidence supporting the identification of two novel species for which we provide molecular diagnostics and propose names. Our analysis indicates that frequent and abundant taxa can be phylogenetically resolved in environmental samples, while rare taxa remain un-captured at our sampling and sequencing intensity. While environmental sequences cannot be automatically translated to species hypothesis, they can be used to generate phylogenetic and ecological evidence supporting species recognition of abundant species without physical specimens.