Fungi Associated with the Earthworm Eisenia fetida

Earthworms are in constant contact with fungi and interact with them in complex ways, which can give rise to diverse fungal communities. We compared the taxonomic composition and community structure of the mycobiota in the digestive tract, coprolites, decomposing bodies, cocoon surface, cocoon contents, and vermicomposting substrate of Eisenia fetida. Fungi were analyzed by culture-based isolation and ITS2 rDNA metabarcoding on the Illumina MiSeq platform. A total of 103 fungal species from 61 genera were identified. The studied habitats were dominated by ascomycetes of the orders Sordariales, Hypocreales, Eurotiales, Pleosporales, Dothideales, and Saccharomycetales and by basidiomycetes of the orders Trichosporonales and Tremellales. Other phyla represented only minor components of the mycobiota. In the earthworm digestive tract, the relative abundance of taxa of Zopfiella, Trichosporon, Penicillium, Aspergillus, Mycothermus, Phialophora, and several other genera that predominated in the substrate consumed by the earthworms decreased, whereas the abundance and diversity of the yeasts Geotrichum, Saccharomyces, Barnettozyma, Hanseniaspora, Candida, Rhodotorula, Sporobolomyces, Leucosporidium, Malassezia, and Solicoccozyma and of the mycelial fungi Fusarium (F. oxysporum and others), Paecilomyces niveus, Tylospora, Ascobolus, Mortierella, and Mucor (M. circinelloides) increased; some of these fungi are capable of yeast-like growth. Fresh coprolites harbored abundant fast-growing, actively sporulating species of Trichoderma, Mucor, Fusarium, Aspergillus, Penicillium, and Rhizopus and contained yeasts of the genera Trichosporon, Apiotrichum, Geotrichum, Saccharomyces, Saccharomycopsis, Pichia, Sporobolomyces, Glaciozyma, Vishniacozyma, and Malassezia, apparently transferred from the earthworm intestine. The cocoon surface carried the same micromycete species as the surrounding substrate. Paecilomyces niveus was frequently detected both on the cocoon surface and in the cocoon contents, whereas Monascus pilosus occurred only occasionally. The mycobiota of decomposing earthworm bodies comprised yeasts and mycelial fungi of the genera Geotrichum, Sungouiella, Trichoderma, Fusarium, Penicillium, and Mucor. The associations of the detected fungi with E. fetida, the possible effects of fungi on earthworms, and directions for further research are discussed.