Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany.
Nat Rev Microbiol. 2019 Jan;17(2):95-109. doi: 10.1038/s41579-018-0116-y.
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.
真菌在陆地和水生环境中都是重要的生态参与者，通过循环有机物质并在营养级之间传递养分。高通量测序（HTS）研究真菌群落正在通过暗示其巨大的——而且在很大程度上尚未绘制的——分类学和功能多样性来重新绘制真菌王国的地图。然而，HTS 方法存在一系列陷阱和潜在的偏差，这就要求在应用和解释 HTS 技术和结果时要谨慎。在这篇综述中，我们提供了 HTS 研究各个方面的概述和实用建议，包括从采样和实验室实践到数据处理和分析。我们还讨论了该领域即将出现的趋势和技术，并总结了 HTS 研究真菌群落和类群的最新和值得注意的结果。我们的综述强调了在真菌群落研究中重现性和公共数据可用性的必要性。如果克服了相关的挑战和概念障碍，HTS 将在真菌学和其他领域提供巨大的可能性。
