Purpose: The objective of this study was to characterize viral communities and assess their diversity in irrigation water and lettuce from the field using metagenomics with high throughput sequencing technology (Illumina sequencing).
Methods: Viruses were concentrated from 100l of irrigation water (n = 6) using hollow fiber ultrafiltration method. For romaine and iceberg lettuce (n = 42), viruses were recovered using Tris-glycine buffer (pH 9.5) followed by precipitation with polyethylene glycol. Viral nucleic acid was extracted and pooled for Illumina sequencing (HiSeq 2500). Bioinformatics approaches were used to analyze the viral metagenomics fingerprints.
Results: Average recovery of bacteriophage P22 from romaine and head lettuce in seeded experiments ranged between 42 and 73%. The proof-of-concept metagenomics study using wastewater showed that 30% of the viruses in sewage were novel. The virome of sewage was dominated by bacteriophages (48%) and human viral pathogens comprised 1% of total known virus sequences. Metagenomics analysis of the viromes of irrigation water and various lettuce samples will be summarized and contrasted to sewage environments.
Significance: The new science of viral metagenomics could be used to discover potential novel viral indicators or viral genetic markers to correlate with the supply of safe and healthy food. This represents a significant advancement in how we evaluate the quality and safety of fresh produce.