Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations.

MSphere
Kasia PiwoszMichaela M Salcher

Abstract

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups,...Continue Reading

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Citations

Aug 25, 2020·Environmental Microbiology·Indranil MukherjeeRohit Ghai
Apr 24, 2020·Molecular Ecology·Clara Ruiz-GonzálezJosep M Gasol
Nov 6, 2020·MSphere·Rebecca E GarnerDavid A Walsh
Mar 23, 2021·Frontiers in Microbiology·Kasia PiwoszKarel Šimek
May 29, 2021·Scientific Reports·Danijela ŠantićStefanija Šestanović

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Methods Mentioned

BETA
PCR
454 sequencing
amplicon sequencing
flow cytometry

Software Mentioned

ggpubr
UCHIME
PRIMER7
PERMANOVA
BLAST
DistML
R
UCHIIME
ggplot2
USEARCH

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