Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing

C.P. Egan; A. Rummel; V. Kokkoris; J. Klironomos; Y. Lekberg; M. Hart

doi:10.1016/j.funeco.2018.01.004

Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing

C.P. Egan, A. Rummel, V. Kokkoris, J. Klironomos, Y. Lekberg, M. Hart

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

© 2018 Elsevier Ltd and British Mycological SocietyCharacterization of arbuscular mycorrhizal (AM) fungal communities increasingly relies on high throughput sequencing (HTS) datasets, but whether sequence data accurately depict AM fungal communities is unknown. We sequenced mock communities of 16 AM fungal morphospecies from six families that varied in relative abundance. To assess sequence variation within fungal individuals, we sequenced single spores of Rhizophagus irregularis. We observed that the relative abundance and taxonomic identity of operational taxonomic units (OTUs) within AM fungal families closely matched expected values, but this decreased at lower taxonomic levels. Multiple OTUs were observed within single spores, suggesting that using OTUs to estimate species richness may inflate richness estimates and reflect sequence variation within individuals. While HTS may introduce some bias in relative abundance estimates and taxonomic identification, we observed high consistency among replicate samples from the same mock community, indicating that these data can inform ecological patterns.

Original language	English
Pages (from-to)	52-64
Journal	Fungal Ecology
Volume	33
DOIs	https://doi.org/10.1016/j.funeco.2018.01.004
Publication status	Published - 1 Jun 2018
Externally published	Yes

Funding

We are grateful for the input and guidance provided by Matthew Settles and the IBEST Genomics Resources Core at the University of Idaho (supported in part by NIH COBRE grant P30GM103324 ) for aiding us with the construction of primers, the PCR workflow (shown in supplementary methods ), and for conducting the sequencing. We are indebted to Maarja Öpik, and our reviewers for detailed comments on a previous drafts which have substantially improved our manuscript. MPG Ranch provided funding to YL, and the Natural Sciences and Engineering Research Council of Canada provided funding to JK and MH. We are grateful for the input and guidance provided by Matthew Settles and the IBEST Genomics Resources Core at the University of Idaho (supported in part by NIH COBRE grant P30GM103324) for aiding us with the construction of primers, the PCR workflow (shown in supplementary methods), and for conducting the sequencing. We are indebted to Maarja Öpik, and our reviewers for detailed comments on a previous drafts which have substantially improved our manuscript. MPG Ranch provided funding to YL, and the Natural Sciences and Engineering Research Council of Canada provided funding to JK and MH.

Funders	Funder number
Core
NIH COBRE
Natural Sciences and Engineering Research Council of Canada	MH
University of Idaho
National Institutes of Health	P30GM103324
Natural Sciences and Engineering Research Council of Canada
Max-Planck-Gesellschaft

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title = "Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing",

abstract = "{\textcopyright} 2018 Elsevier Ltd and British Mycological SocietyCharacterization of arbuscular mycorrhizal (AM) fungal communities increasingly relies on high throughput sequencing (HTS) datasets, but whether sequence data accurately depict AM fungal communities is unknown. We sequenced mock communities of 16 AM fungal morphospecies from six families that varied in relative abundance. To assess sequence variation within fungal individuals, we sequenced single spores of Rhizophagus irregularis. We observed that the relative abundance and taxonomic identity of operational taxonomic units (OTUs) within AM fungal families closely matched expected values, but this decreased at lower taxonomic levels. Multiple OTUs were observed within single spores, suggesting that using OTUs to estimate species richness may inflate richness estimates and reflect sequence variation within individuals. While HTS may introduce some bias in relative abundance estimates and taxonomic identification, we observed high consistency among replicate samples from the same mock community, indicating that these data can inform ecological patterns.",

author = "C.P. Egan and A. Rummel and V. Kokkoris and J. Klironomos and Y. Lekberg and M. Hart",

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doi = "10.1016/j.funeco.2018.01.004",

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TY - JOUR

T1 - Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing

AU - Egan, C.P.

AU - Rummel, A.

AU - Kokkoris, V.

AU - Klironomos, J.

AU - Lekberg, Y.

AU - Hart, M.

PY - 2018/6/1

Y1 - 2018/6/1

N2 - © 2018 Elsevier Ltd and British Mycological SocietyCharacterization of arbuscular mycorrhizal (AM) fungal communities increasingly relies on high throughput sequencing (HTS) datasets, but whether sequence data accurately depict AM fungal communities is unknown. We sequenced mock communities of 16 AM fungal morphospecies from six families that varied in relative abundance. To assess sequence variation within fungal individuals, we sequenced single spores of Rhizophagus irregularis. We observed that the relative abundance and taxonomic identity of operational taxonomic units (OTUs) within AM fungal families closely matched expected values, but this decreased at lower taxonomic levels. Multiple OTUs were observed within single spores, suggesting that using OTUs to estimate species richness may inflate richness estimates and reflect sequence variation within individuals. While HTS may introduce some bias in relative abundance estimates and taxonomic identification, we observed high consistency among replicate samples from the same mock community, indicating that these data can inform ecological patterns.

AB - © 2018 Elsevier Ltd and British Mycological SocietyCharacterization of arbuscular mycorrhizal (AM) fungal communities increasingly relies on high throughput sequencing (HTS) datasets, but whether sequence data accurately depict AM fungal communities is unknown. We sequenced mock communities of 16 AM fungal morphospecies from six families that varied in relative abundance. To assess sequence variation within fungal individuals, we sequenced single spores of Rhizophagus irregularis. We observed that the relative abundance and taxonomic identity of operational taxonomic units (OTUs) within AM fungal families closely matched expected values, but this decreased at lower taxonomic levels. Multiple OTUs were observed within single spores, suggesting that using OTUs to estimate species richness may inflate richness estimates and reflect sequence variation within individuals. While HTS may introduce some bias in relative abundance estimates and taxonomic identification, we observed high consistency among replicate samples from the same mock community, indicating that these data can inform ecological patterns.

U2 - 10.1016/j.funeco.2018.01.004

DO - 10.1016/j.funeco.2018.01.004

M3 - Article

SN - 1754-5048

VL - 33

SP - 52

EP - 64

JO - Fungal Ecology

JF - Fungal Ecology

ER -

Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing

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