The Risk of Pathogens Associated with Seed Potatoes (Solanum tuberosum) Imported to Sri Lanka : A Metagenomic Approach

Abstract

Potato is a major global crop and transmission of tuber borne diseases is a major cause of yield reduction in potato cultivation. The potato tuber harbors an array of undescribed microorganisms which may include pathogens of quarantine importance. Therefore, many countries follow stringent quarantine regulations to prevent the entry of pests with the imported potato seed stocks. In this study, 16S rDNA-based meta-genomic analyses was carried out to detect the microbial pathogens and to characterize the bacterial diversity associated with the potato seed tuber consignments imported to Sri Lanka for cultivation purposes. DNA extracted from the potato tubers were sequenced by using Ion Torrent Next Generation Sequencing (NGS) technology and meta-genomic studies were performed by amplifying a ~ 400 bp V1-V2 hypervariable region of the prokaryotic 16S rRNA gene. The computational steps required to analyze the NGS data of 16S rDNA were carried out by using the MG-RAST online pipeline which implements workflows for sequence alignment with the SILVA SSU ribosomal RNA database. The sequence analysis profiled all available bacteria within each sample. Bacteria representing Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetaceae and Sphirochaetales phyla were detected in varying abundances. PCR with the species specific primers and sequencing confirmed the presence of Ralstonia solanacearum, Pectobacterium caratovorum, Streptomyces scabies and Xanthomonas oryzae pv. oryzae which are pathogens of quarantine importance.