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

• Type: Article in International Scientific Journal
• Date: 2021

Authors

Azevedo Silva, D (Author) Other; Rasmussen, JA (Author) Other; Carneiro, M (Author) Other; Gilbert, MTP (Author) Other; Azevedo, H (Author) FCUP

Journal

Title: Australian Journal of Grape and Wine Research

Vol. 27

Pages: 519-526

ISSN: 1322-7130

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 3 Citations

Scopus - 4 Citations

Other information

Authenticus ID: P-00V-3DJ

DOI: 10.1111/ajgw.12508

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8