PRIN ADAPT MICROBIOLOGY _ Campania

Published: 13 March 2024| Version 1 | DOI: 10.17632/6jcyrwj2gh.1
Contributor:
massimo iorizzo

Description

Fastq files of fungal community present in harvested grapes were analysed by a culture-independent approach using next-generation sequencing (NGS). Grape berries of Aglianico and Cabernet were collected during the 2020 growing season at the full ripening stage in a site of Campania region. In total, two experimental samples were considered: Aglianico Campania (AC) and Cabernet Campania (CC).

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Berries were collected during the 2020 growing season at the full ripening stage. Thirty clusters were harvested from different positions of the vineyard and from random positions on the plant to ensure the representation of the entire vineyard. At least ten berries were randomly selected from different parts of the cluster, avoiding those with visible damage and/or signs of pathogen infection, and pooled with berries from the other plants. For subsequent analyses, three independent pools (biological replicates) of 50 whole berries were selected, immediately frozen in liquid nitrogen, and stored at -80°C for subsequent analyses. For each analysis, two experimental samples were considered: Aglianico Campania (AC), and Cabernet Campania (CC). Fungal community composition was analysed by a culture-independent approach using next-generation sequencing (NGS). The grape samples from every vineyard were collected in duplicate, immediately transported to the laboratory and processed. Total genomic DNA was extracted using the Stool DNA Isolation Kit (Norgen, Biotek Corp., Thorold, ON, Canada) according to the manufacturer's instructions. The concentration and purity of the extracted nucleic acids were visualised and quantified, after agarose gel electrophoresis, by Nanodrop (NanoDropTM 2000/2000c; Thermo Fisher Scientific, Italy). DNA quantity was standardized to a concentration of 10 ng/μl. The ITS2 (internal transcribed spacer) region of the rRNA was amplified using primers 2024F and 2409R. Amplicons were sequenced using the Illumina MiSeq PE300 platform (Illumina, San Diego, CA, USA) at Biodiversa s.r.l. (Rovereto, Italy). Adapter sequences were removed using Cutadapt (Martin, 2011). Read quality was assessed using DADA2 (Callahan et al., 2016). The taxonomic references were assigned using trained OTUs at 99% from UNITE database version 8.2 (https://unite.ut.ee) within Qiime2 tools version 2020.2 (https://qiime2.org).

Institutions

Universita degli Studi del Molise Dipartimento Agricoltura Ambiente e Alimenti

Categories

Microbiology, Metagenomics, Grape, Berry Fruit

Funding

Ministero dell’Istruzione, dell’Università e della Ricerca

Research Projects of National Interest (PRIN) ADAPT - influence of agro-climatic conditions on the microbiome and genetic expression of grapevines for the production of red wines: a multidisciplinary approach (2017M83XFJ - CUP H34I19000590001)

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