School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA.
Biology Department, Utah Valley University, Orem, UT, USA.
Microb Ecol. 2022 Jan;83(1):48-57. doi: 10.1007/s00248-021-01730-x. Epub 2021 Mar 20.
To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.
为了研究微生物（包括真菌）的生物地理学和其他生态学模式，科学家们一直将操作分类单元（OTUs）用作物种或物种假说的代表。然而，当按照 97%的序列相似性定义（在细菌中，如公认的条形码基因座 16S，或在真菌中，如 ITS）时，这些 OTUs 会掩盖生物地理学模式，掩盖分类多样性，并阻碍元分析。扩增子序列变体（ASVs）被提议用来解决所有这些问题，并且在细菌中已经证明了这一点。分析 ASVs 刚刚成为真菌研究中的一种常见做法，但是否在真菌中发现的使用这种方法的细菌研究中的好处仍然不清楚。在这里，我们通过分析 ITS1 扩增子测序数据作为 ASVs 并探索生态学模式，对夏威夷真菌进行了元分析。这些调查跨越了三个岛屿群和五个生态系统，合并为第一个综合的夏威夷真菌宏基因组 ASV 数据库。我们的结果表明，ASVs 可用于组合真菌 ITS 调查，提高可重复性，并保持使用 OTUs 观察到的广泛的生态模式，包括多样性排序。此外，构成我们数据库中一些最常见 OTUs 的 ASVs 揭示了一些岛屿特有种，表明传统的 OTU 聚类可能会掩盖重要的生物地理学模式。我们建议未来的真菌研究，特别是那些旨在评估生物地理学的研究，分析 ASVs 而不是 OTUs。我们得出结论，与细菌研究类似，ASVs 提高了真菌研究的可重复性和数据共享性。
