Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

MSphere
Sydney I Glassman, Jennifer B H Martiny

Abstract

Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, ...Continue Reading

References

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Citations

Feb 5, 2019·Microbial Ecology·Stephanie N KivlinJennifer A Rudgers
Feb 12, 2019·Scientific Reports·Blanca Vera-GargalloAntonio Ventosa
Mar 6, 2019·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Stefan A BoersJohn P Hays
Aug 17, 2019·The ISME Journal·Natalia García-GarcíaFernando Puente-Sánchez
Nov 20, 2019·Proceedings of the National Academy of Sciences of the United States of America·Andrew J TanentzapThorsten Dittmar
Oct 7, 2019·BJOG : an International Journal of Obstetrics and Gynaecology·J L O'CallaghanE S Pelzer
Nov 7, 2019·Ecology and Evolution·Arthur EscalasJizhong Zhou
Jun 5, 2020·American Journal of Botany·Karen W HughesTeresa Iturriaga
Jun 20, 2020·The New Phytologist·Jean C Rodriguez-RamosNadir Erbilgin
Nov 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Sydney I GlassmanJennifer B H Martiny
Feb 6, 2020·Nature Ecology & Evolution·Manuel Delgado-BaquerizoBrajesh K Singh
Aug 28, 2020·Frontiers in Microbiology·Jorge T AntunesVitor Vasconcelos
Sep 14, 2019·Nature Communications·Keara L GradyAshley Shade
Dec 10, 2019·GigaScience·Julien Tremblay, Etienne Yergeau
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Dec 21, 2019·Journal of Animal Science and Biotechnology·Feilong DengJiangchao Zhao
Jan 5, 2020·Nature Ecology & Evolution·Thorsten ThiergartStéphane Hacquard
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Jan 21, 2019·Environment International·William A Gerhard, Claudia K Gunsch
Nov 13, 2019·Current Opinion in Microbiology·Ashley Shade, Nejc Stopnisek
Mar 21, 2021·Microbial Ecology·Laura TiptonNicole A Hynson
Apr 25, 2021·Ecology Letters·Gabriel Reuben Smith, Kabir G Peay
Aug 19, 2021·Microbial Ecology·Francisco PascoalCatarina Magalhães
Aug 28, 2021·Microorganisms·Marie-Charlotte CheutinJean-Christophe Auguet

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Methods Mentioned

BETA
amplicon sequencing
PCR

Software Mentioned

NMDS
PERMANOVA
UPARSE

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