Tracking Microbes from Irrigation Water to Crops: The Potential of Metagenomics and Meta-Transcriptomics

Irrigated crops may harbor microbes from irrigation water that may be deleterious and pose risks to consuming humans and animals. To provide good and quality food void of contamination with harmful pathogens and reduce foodborne diseases, there exists the need to continuously monitor and trace the tran¬sition of microbes from irrigation water to crops. Traditional methods of culturing microbes provided the basic knowledge of the presence of microbes and their transition from irrigation water to the crop however, they are low throughput and cumbersome. The advent of new technologies that can provide high-through-put data have made monitoring of microbes in irrigation water easier generating multitudes of data for both culturable and fastidious microbes. Metagenomics and meta-transcriptomics techniques are promising as they boost generate massive data with less effort than the case of traditional methods. Their application in tracing microbes from irrigation water to crops showed that the crops could harbor harmful microbes pres¬ent in irrigation water. However, further studies are required to improve databases, particularly for viruses and protozoa, standardizing metagenomics, and meta-transcriptomics data analysis protocols.