Metagenomic analysis of endophytic bacteria in seed potato (Solanum tuberosum)

Abstract

To date, the association of potato tuber microbiota is poorly understood. In this study, the endophytic bacterial flora of seed potato tubers was identified and the diversity of healthy and unhealthy tubers was compared. Metagenomic DNA extracted from healthy and unhealthy samples of seed potato tubers was used for the analysis of microbial communities. Next generation sequencing of the ∼460 bp v3–v4 region of the 16S rRNA gene was carried out using the Illumina Miseq platform. The data were analysed using the Divisive Amplicon Denoising Algorithm 2 pipeline. Sequence analysis of the potato metagenome identified amplicon sequence variants (ASVs) assigned to 745 different taxa belonging to eight Phyla: Firmicutes (46.2%), Proteobacteria (36.9%), Bacteroidetes (1.8%), Actinobacteria (0.1%), Tenericutes (0.005%), Saccharibacteria (0.003%), Verrucomicrobiota (0.003%), and Acidobacteria (0.001%). In healthy seed potato tubers, 55–99% of ASVs belonged to Firmicutes, including Bacillus, Salinibacillus, Staphylococcus, Lysinibacillus, Paenibacillus, and Brevibacillus genera within the taxonomic order Bacillales. However, in the visually unhealthy tubers, only 0.5–3.9% of ASVs belonged to Firmicutes while 84.1–97% of ASVs belonged to Proteobacteria. This study highlights that diverse bacterial communities colonize potato tubers, which contributes to the understanding of plant–microbe interactions and underscores the significance of metagenomic approaches in agricultural research.