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Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach

Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factor...

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Autores principales: Singh, Prashant, Santoni, Sylvain, This, Patrice, Péros, Jean-Pierre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313654/
https://www.ncbi.nlm.nih.gov/pubmed/30248973
http://dx.doi.org/10.3390/microorganisms6040096
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author Singh, Prashant
Santoni, Sylvain
This, Patrice
Péros, Jean-Pierre
author_facet Singh, Prashant
Santoni, Sylvain
This, Patrice
Péros, Jean-Pierre
author_sort Singh, Prashant
collection PubMed
description Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factors (i.e., at different geographic locations) on the phyllosphere has never been studied and is the main objective of this report. Using high throughput short amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS), we analyzed the impacts of genotypes of Vitis Vinifera (coming from three genetic pool), on the microbial (bacterial and fungal) assemblage in the phyllosphere. First, we performed the analysis of the phyllosphere microbiome while using fifteen genotypes that were chosen to maximize intra-specific diversity and grown in two Mediterranean vineyards. Then, the same analysis was performed on five commercially important varieties of Vitis vinifera that were sampled from three different French agro-climatic zones (or terroir: a combination of climate, soils, and human practices). Our study revealed that, at a particular geographic location, genotypes have an impact on microbial assemblage in the phyllosphere and carposphere of leaf and fruit (or berries), respectively, which is more prominent on the carposphere but the effect of terroir was much stronger than the genotype when the leaf phyllosphere of five grapevine varieties grown in different agro-climatic zones was compared. Impacts of the season and exterior plant organs (leaf and berries) on microbial taxa structuring in the phyllosphere was also assessed and presented in this report.
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spelling pubmed-63136542019-01-04 Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach Singh, Prashant Santoni, Sylvain This, Patrice Péros, Jean-Pierre Microorganisms Article Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factors (i.e., at different geographic locations) on the phyllosphere has never been studied and is the main objective of this report. Using high throughput short amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS), we analyzed the impacts of genotypes of Vitis Vinifera (coming from three genetic pool), on the microbial (bacterial and fungal) assemblage in the phyllosphere. First, we performed the analysis of the phyllosphere microbiome while using fifteen genotypes that were chosen to maximize intra-specific diversity and grown in two Mediterranean vineyards. Then, the same analysis was performed on five commercially important varieties of Vitis vinifera that were sampled from three different French agro-climatic zones (or terroir: a combination of climate, soils, and human practices). Our study revealed that, at a particular geographic location, genotypes have an impact on microbial assemblage in the phyllosphere and carposphere of leaf and fruit (or berries), respectively, which is more prominent on the carposphere but the effect of terroir was much stronger than the genotype when the leaf phyllosphere of five grapevine varieties grown in different agro-climatic zones was compared. Impacts of the season and exterior plant organs (leaf and berries) on microbial taxa structuring in the phyllosphere was also assessed and presented in this report. MDPI 2018-09-21 /pmc/articles/PMC6313654/ /pubmed/30248973 http://dx.doi.org/10.3390/microorganisms6040096 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Singh, Prashant
Santoni, Sylvain
This, Patrice
Péros, Jean-Pierre
Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
title Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
title_full Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
title_fullStr Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
title_full_unstemmed Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
title_short Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
title_sort genotype-environment interaction shapes the microbial assemblage in grapevine’s phyllosphere and carposphere: an ngs approach
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313654/
https://www.ncbi.nlm.nih.gov/pubmed/30248973
http://dx.doi.org/10.3390/microorganisms6040096
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