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Review
. 2019 Jan;17(2):95-109.
doi: 10.1038/s41579-018-0116-y.

Mycobiome diversity: high-throughput sequencing and identification of fungi

R Henrik Nilsson  1 , Sten Anslan  2 , Mohammad Bahram  3 , Christian Wurzbacher  4 , Petr Baldrian  5 , Leho Tedersoo  6
Affiliations
Review

Mycobiome diversity: high-throughput sequencing and identification of fungi

R Henrik Nilsson et al. Nat Rev Microbiol. 2019 Jan.

Abstract

Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.

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References

    1. Hawksworth, D. L. & Lücking, R. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spectr. 5, 4 (2017).
    1. Tedersoo, L. et al. High-level classification of the fungi and a tool for evolutionary ecological analyses. Fung. Div. 90, 135–159 (2018).
    1. Berbee, M. L., James, T. Y. & Strullu-Derrien, C. Early diverging fungi: diversity and impact at the dawn of terrestrial life. Ann. Rev. Microbiol. 71, 41–60 (2017). This eye-opening paper is a mycological must-read that substantially broadens the scope of what fungi are and which fungi should be included in both HTS-based efforts and general mycological parlance.
    1. Peay, K. G., Kennedy, P. G. & Talbot, J. M. Dimensions of biodiversity in the Earth mycobiome. Nat. Rev. Microbiol. 14, 434–447 (2016).
    1. Tedersoo, L. & Nilsson, R. H. in Molecular Mycorrhizal Symbiosis (ed. Martin, F.) 301–322 (Wiley, Hoboken, 2016).

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