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Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography

  • Fungal Microbiology
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Abstract

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.

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Acknowledgments

The authors would like to thank Dr. Nhu Nguyen for contributing previously unpublished data. We would also like to thank Katie Lund for assisting with sample processing. This research was made possible in part by an award to A.S.A. and N.A.H. from the W.M. Keck Foundation and The National Science Foundation, award numbers 1556856 & 1255972. L.T. was funded by the Alfred P. Sloan Foundation Microbiome of the Built Environment Postdoctoral Fellowship and would like to thank the Hawaii Data Science Institute and the UH Cyber Infrastructure team for their HPC support.

Data Accessibility and Code Availability

DNA sequences are in the NCBI SRA under the accession numbers shown in Table 1. Final ASV table, sample metadata, and code can be found at https://github.com/ltipton/HIMycobiome. Complete ASV database will be uploaded to the Hawaii Data Science Institute repository at https://himycobiome.its.hawaii.edu.

Funding

This research was made possible in part by an award to A.S.A. and N.A.H. from the W.M. Keck Foundation and The National Science Foundation, award numbers 1556856 & 1255972. L.T. was funded by the Alfred P. Sloan Foundation Microbiome of the Built Environment Postdoctoral Fellowship.

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Authors and Affiliations

  1. School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA

    Laura Tipton

  2. Biology Department, Utah Valley University, Orem, UT, USA

    Geoffrey L. Zahn

  3. Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

    John L. Darcy

  4. School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, USA

    Anthony S. Amend

  5. Pacific Biosciences Research Center, University of Hawai‘i at Mānoa, Honolulu, HI, USA

    Nicole A. Hynson

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  1. Laura Tipton
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  2. Geoffrey L. Zahn
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  4. Anthony S. Amend
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  5. Nicole A. Hynson
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Contributions

N.A.H., A.S.A., and L.T. designed the research; G.L.Z. and A.S.A. performed the research; L.T., J.L.D., and G.Z. analyzed the data; all authors contributed to manuscript preparation and editing.

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Correspondence to Nicole A. Hynson.

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Tipton, L., Zahn, G.L., Darcy, J.L. et al. Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography. Microb Ecol 83, 48–57 (2022). https://doi.org/10.1007/s00248-021-01730-x

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