TY - JOUR

T1 - Feasibility of applying shotgun metagenomic analyses to grapevine leaf, rhizosphere and soil microbiome characterisation

AU - Azevedo-Silva, D.

AU - Rasmussen, J. A.

AU - Carneiro, M.

AU - Gilbert, M. T. P.

AU - Azevedo, H.

N1 - Funding Information: Financial support was provided by Fundação para a Ciência e Tecnologia (FCT/MCTES) to Dr Herlander Azevedo (CEECIND/00399/2017) and Dr Miguel Carneiro (CEECINST/00014/2018), and by a Danish National Research Foundation award DNRF143 to Professor M. Thomas P. Gilbert. Publisher Copyright: © 2021 Australian Society of Viticulture and Oenology Inc.

PY - 2021

Y1 - 2021

N2 - Background and Aims: The characterisation of plant microbiomes using metabarcoding strategies is expected to be progressively replaced by shotgun metagenomic (SMg) approaches. In the present report we explore the potential of applying SMg to grapevine leaf, rhizosphere and soil samples. Methods and Results: Our strategy involved combining a single method for column-based DNA extraction of multiple tissues, with sequencing using the BGISEQ short-read next-generation sequencing platform. This study details aspects of DNA isolation, library construction, sequencing and early bioinformatics treatment of read data, including the use of subsampling as a proxy for detection of sample microbial proportions. The combination of an innovative sequencing platform with recent mapping tools allowed for the characterisation of the microbiome associated with the grapevine leaf, rhizosphere and adjacent soil. Conclusions: We coupled a robust single extraction/library preparation protocol suitable for contrasting samples, with cost-effective BGISEQ short-read next-generation sequencing technology, to generate a landscape of grapevine-associated microbial diversity. Significance of the Study: Shotgun metagenomics is emerging as a state-of-the-art approach to grapevine microbiome characterisation. The present report provides a detailed and technical roadmap targeting multiple aspects of this important approach.

AB - Background and Aims: The characterisation of plant microbiomes using metabarcoding strategies is expected to be progressively replaced by shotgun metagenomic (SMg) approaches. In the present report we explore the potential of applying SMg to grapevine leaf, rhizosphere and soil samples. Methods and Results: Our strategy involved combining a single method for column-based DNA extraction of multiple tissues, with sequencing using the BGISEQ short-read next-generation sequencing platform. This study details aspects of DNA isolation, library construction, sequencing and early bioinformatics treatment of read data, including the use of subsampling as a proxy for detection of sample microbial proportions. The combination of an innovative sequencing platform with recent mapping tools allowed for the characterisation of the microbiome associated with the grapevine leaf, rhizosphere and adjacent soil. Conclusions: We coupled a robust single extraction/library preparation protocol suitable for contrasting samples, with cost-effective BGISEQ short-read next-generation sequencing technology, to generate a landscape of grapevine-associated microbial diversity. Significance of the Study: Shotgun metagenomics is emerging as a state-of-the-art approach to grapevine microbiome characterisation. The present report provides a detailed and technical roadmap targeting multiple aspects of this important approach.

KW - BGISEQ short-read next-generation sequencing platform

KW - DNA extraction

KW - grapevine

KW - microbiome

KW - shotgun metagenomics

U2 - 10.1111/ajgw.12508

DO - 10.1111/ajgw.12508

M3 - Journal article

AN - SCOPUS:85108249589

VL - 27

SP - 519

EP - 526

JO - Australian Journal of Grape and Wine Research

JF - Australian Journal of Grape and Wine Research

SN - 1322-7130

IS - 4

ER -