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ARS Home » Southeast Area » Poplarville, Mississippi » Southern Horticultural Research » Research » Research Project #434978

Research Project: Impact of Drought and High Soil pH on Blueberries rhizosphere Microbiome

Location: Southern Horticultural Research

Project Number: 6062-21000-010-10-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jun 4, 2018
End Date: Jun 8, 2020

Objective:
The purpose of the project is to obtain basic knowledge about the microbial community composition on roots of different Vaccinium species. The expected results will complement the conventional and molecular breeding efforts aimed at the development of blueberry cultivar with improved level of tolerance to drought and high soil pH.

Approach:
Two accessions of each of Vaccinium (V.) darrowii, V. virgatum, V. corymbosum, and V. arboreum will be grown in a greenhouse under two irrigation regimes (optimal and drought conditions). For each accession, six different plants (n = 6) will be sampled and processed to extract the rhizosphere soil DNA. Approximately ten grams of roots will be collected from each experimental unit and used to extract the microbial DNA. Barcoded amplicons will be generated from the extracted rhizosphere DNA by Polymerase Chain Reaction (PCR) with primers targeting the V4 region of bacterial 16S rRNA, the V4 region of eukaryotic 18S rRNA, and the internal transcribed spacer (ITS) 2 region of fungi. The amplicons will be purified, quantified, and sequenced (2 × 300 bp). The sequence data will be processed and the paired-end reads will be merged. Operational taxonomic units (OTUs) will be characterized by matching to the RDP 16S rRNA database (11 release), 18S rRNA database , and the UNITE database of the fungal ITS sequences. Reads will be subsequently mapped back to OTUs to determine OTU abundance for each sample. The R package Phyloseq will be used to generate nonmetric multidimensional scaling (NMDS) plots to visualize the most abundant phyla in samples acquired from different species/accession of Vaccinium.