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

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, we need not question the validity of results based on OTUs. Microbial ecologists have made exceptional improvements in our understanding of microbiomesmore » in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.« less

Authors:

Glassman, Sydney I. ^[1]; Martiny, Jennifer B. H. ^[2]; Tringe, ed., Susannah Green

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+ Show Author Affiliations

1. Department of Ecology and Evolutionary Biology, University of California—Irvine, Irvine, California, USA, Department of Microbiology and Plant Pathology, University of California—Riverside, Riverside, California, USA
2. Department of Ecology and Evolutionary Biology, University of California—Irvine, Irvine, California, USA

Publication Date:

2018-08-29

Research Org.:

Univ. of California, Irvine, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1461716

Alternate Identifier(s):

OSTI ID: 1511016

Grant/Contract Number:  

SC0016410

Resource Type:

Published Article

Journal Name:

mSphere

Additional Journal Information:

Journal Name: mSphere Journal Volume: 3 Journal Issue: 4; Journal ID: ISSN 2379-5042

Publisher:

American Society for Microbiology

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Illumina MiSeq, bacteria, exact sequence variants (ESVs), fungi, microbial ecology, operational taxonomic units (OTUs)