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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-8819139 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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