A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition

• Published in: Fungal ecology Vol. 20; pp. 175 - 185
• Main Authors: Siddique, A.B., Unterseher, M.
• Format: Journal Article
• Language: English
• Published: Elsevier Ltd 01.04.2016
• Subjects: autumn; Biodiversity; case studies; community structure; cost effectiveness; DNA; Ecology; Elevation; Endophytes; Environmental change; environmental factors; European beech; Fagus sylvatica; Fagus sylvatica subsp. sylvatica; fungal communities; fungi; habitats; High throughput sequencing; high-throughput nucleotide sequencing; Illumina sequencing; internal transcribed spacers; Leaf-inhabiting microfungi; leaves; Metabarcoding; physiological state; Alps region; Germany; Metabarcoding; Elevation; High throughput sequencing; Leaf-inhabiting microfungi; European beech; Endophytes; Environmental change; Ecology; Biodiversity; Illumina sequencing; Fagus sylvatica
• ISSN: 1754-5048; 1878-0083
• DOI: 10.1016/j.funeco.2015.12.009

We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.