How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity

TRUONG, CAMILLE; MUJIC, ALIJA B.; HEALY, ROSANNE; KUHAR, FRANCISCO; FURCI, GIULIANA; TORRES, DANIELA; NISKANEN, TUULA; SANDOVAL-LEIVA, PABLO A.; FERNÁNDEZ, NATALIA; ESCOBAR, JULIO M.; MORETTO, ALICIA; PALFNER, GÖTZ; PFISTER, DONALD; NOUHRA, EDUARDO; SWENIE, RACHEL; SÁNCHEZ-GARCÍA, MARISOL; MATHENY, P. BRANDON; SMITH, MATTHEW E.

NEW PHYTOLOGIST

WILEY-BLACKWELL PUBLISHING, INC

Año: 2017 vol. 214 p. 913 - 919

0028-646X

The Southern Hemisphere harbors many unique fungal lineagesthat are absent from the Northern Hemisphere (Tedersoo&Smith,2013; Tedersoo et al., 2014). In southern South America, recentstudies based on environmental sequences have detected severalpreviously unknown fungal lineages, thereby demonstrating thatfungal diversity is probably much higher than presently known(Nouhra et al., 2013; Geml et al., 2014; Roy et al., 2017).As part of a project investigating ectomycorrhizal (ECM) fungiof southern South America, our team collected 1430 fungal fruitingbodies during four collecting expeditions, equaling c. 50 d with 3?4collectors per day (Supporting Information Methods S1). Weprimarily collected ECM fungi in temperate forests dominated byNothofagaceae but also opportunistically collected nonECMfungi. Vouchered specimens were photographed and dried forfuture study. Internal transcribed spacerrDNAsequences (ITS, e.g.ITS1-5.8S-ITS2) were obtained from a representative selection of957 specimens using the Extract-N-AmpPlant kit (Sigma-Aldrich)for rapid DNA extraction and amplification. ITS sequences wereclustered into operational taxonomic units (OTUs) at 97?99%similarity against the UNITE ?species hypothesis? dynamicdatabase (Abarenkov et al., 2010a; K~oljalg et al., 2013) usingQIIME 1.9.1 (Caporaso et al., 2010). Sequences that did notcorrespond to an existing ?species hypothesis? in the referencedatabase were subsequently clustered de novo at 97% similarity(Methods S1). One representative sequence per OTU wassubsequently compared to UNITE+INSD (UNITE and theInternational Nucleotide Sequence Databases) using MEGABLASTon the PLUTOF workbench (Abarenkov et al., 2010b).