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Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns

Next-generation sequencing is one of the most popular and cost-effective ways of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are limited, as they result in relative abundance profiles of microbial taxa, which does not represe...

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Autores principales: Azarbad, Hamed, Tremblay, Julien, Bainard, Luke D., Yergeau, Etienne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8819139/
https://www.ncbi.nlm.nih.gov/pubmed/35140695
http://dx.doi.org/10.3389/fmicb.2021.798023
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author Azarbad, Hamed
Tremblay, Julien
Bainard, Luke D.
Yergeau, Etienne
author_facet Azarbad, Hamed
Tremblay, Julien
Bainard, Luke D.
Yergeau, Etienne
author_sort Azarbad, Hamed
collection PubMed
description Next-generation sequencing is one of the most popular and cost-effective ways of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are limited, as they result in relative abundance profiles of microbial taxa, which does not represent actual abundance in the environment. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that changes in the relative abundance of major microbial phyla do not necessarily follow the same pattern as the estimated quantitative abundance. Most of the bacterial phyla linked with the rhizosphere of plants grown in soil with no history of water stress showed enrichment patterns in their estimated absolute abundance, which was in contradiction with the trends observed in the relative abundance data. However, in the case of the fungal groups (except for Basidiomycota), such an enrichment pattern was not observed and the abundance of fungi remained relatively unchanged under different soil water stress history when estimated absolute abundance was considered. Comparing relative and estimated absolute abundances of dominant bacterial and fungal phyla, as well as their correlation with the functional processes in the rhizosphere, our results suggest that the estimated absolute abundance approach gives a different and more realistic perspective than the relative abundance approach. Such a quantification approach provides complementary information that helps to better understand the rhizosphere microbiomes and their associated ecological functional processes.
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spelling pubmed-88191392022-02-08 Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns Azarbad, Hamed Tremblay, Julien Bainard, Luke D. Yergeau, Etienne Front Microbiol Microbiology Next-generation sequencing is one of the most popular and cost-effective ways of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are limited, as they result in relative abundance profiles of microbial taxa, which does not represent actual abundance in the environment. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that changes in the relative abundance of major microbial phyla do not necessarily follow the same pattern as the estimated quantitative abundance. Most of the bacterial phyla linked with the rhizosphere of plants grown in soil with no history of water stress showed enrichment patterns in their estimated absolute abundance, which was in contradiction with the trends observed in the relative abundance data. However, in the case of the fungal groups (except for Basidiomycota), such an enrichment pattern was not observed and the abundance of fungi remained relatively unchanged under different soil water stress history when estimated absolute abundance was considered. Comparing relative and estimated absolute abundances of dominant bacterial and fungal phyla, as well as their correlation with the functional processes in the rhizosphere, our results suggest that the estimated absolute abundance approach gives a different and more realistic perspective than the relative abundance approach. Such a quantification approach provides complementary information that helps to better understand the rhizosphere microbiomes and their associated ecological functional processes. Frontiers Media S.A. 2022-01-24 /pmc/articles/PMC8819139/ /pubmed/35140695 http://dx.doi.org/10.3389/fmicb.2021.798023 Text en Copyright © 2022 Azarbad, Tremblay, Bainard and Yergeau. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Azarbad, Hamed
Tremblay, Julien
Bainard, Luke D.
Yergeau, Etienne
Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
title Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
title_full Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
title_fullStr Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
title_full_unstemmed Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
title_short Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
title_sort relative and quantitative rhizosphere microbiome profiling results in distinct abundance patterns
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8819139/
https://www.ncbi.nlm.nih.gov/pubmed/35140695
http://dx.doi.org/10.3389/fmicb.2021.798023
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