Exploring Taxonomic and Functional Microbiome of Hawaiian Stream and Spring Irrigation Water Systems Using Illumina and Oxford Nanopore Sequencing Platforms

Abstract

Irrigation water is a potential source of contamination that carries plant and foodborne human pathogens and provides a niche for survival and proliferation of microbes in agricultural settings. This project investigated bacterial communities and their functions in the irrigation water from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and tank stored water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phyla in river stream source and associated wet taro field water samples. Cyanobacteria was also a dominant phylum from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. Whereas samples sequenced for full length 16S rRNA and shotgun metagenome, clearly illustrated that Oxford Nanopore MinION is a better choice to classify the microbes to the genus and species levels. In terms of functional analyses, only 12% of the genes were shared by two consortia. Total 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Description of microbial communities and their functions are essential for the development of better water management strategies to produce safer fresh produce and to protect plant, animal, human and environmental health. This project identified analytical tools to study microbiome of irrigation water.