Data from: Finding flies in the mushroom soup: host specificity of fungus-associated communities revisited with a novel molecular method

Fruiting bodies of fungi constitute an important resource for thousands of
other taxa. The structure of these diverse assemblages has traditionally
been studied with labour-intensive methods involving cultivation and
morphology-based species identification, to which molecular information
might offer convenient complements. To overcome challenges in DNA
extraction and PCR associated with the complex chemical properties
fruiting bodies, we developed a pipeline applicable for extracting
amplifiable total DNA from soft fungal samples of any size. Our protocol
purifies DNA in two sequential steps: (1) initial salt-isopropanol
extraction of all nucleic acids in the sample is followed by (2) an extra
clean-up step using solid-phase reversible immobilization (SPRI) magnetic
beads. The protocol proved highly efficient, with practically all of our
samples — regardless of biomass or other properties — being successfully
PCR amplified using metabarcoding primers and subsequently sequenced. As a
proof-of-concept, we apply our methods to address a topical ecological
question: is host specificity a major characteristic of fungus-associated
communities, i.e., do different fungus species harbour different
communities of associated organisms? Based on an analysis of 312 fungal
fruiting bodies representing ten species in five genera from three orders,
we show that molecular methods are suitable for studying this rich natural
microcosm. Comparing to previous knowledge based on rearing and
morphology-based identifications, we find a species-rich assemblage
characterized by a low degree of host specialization. Our method opens up
new horizons for molecular analyses of fungus-associated interaction webs
and communities.