Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms

Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank 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 phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples 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. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.

Automated summary

Irrigation water serves as a common source of contamination in agriculture, carrying plant and foodborne human pathogens and providing a habitat for microbial proliferation. This study investigated the bacterial communities and their functions in irrigation water from wetland taro farms in Hawaii, using different DNA sequencing platforms. The results showed that Illumina reads provided comprehensive taxonomic classification, with Proteobacteria being the most abundant phylum in stream source and associated water samples. Cyanobacteria dominated tank and spring water samples, while Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, a significant portion of the short amplicon reads remained unclassified at the species level. In contrast, Oxford Nanopore MinION was better for microbe classification at the genus and species levels, while shotgun metagenome data did not yield reliable taxonomic classification results. Functional analysis revealed a limited overlap of genes between consortia and the presence of antibiotic resistance genes. Comprehensive understanding of microbial communities and their functions is crucial for developing effective water management strategies to ensure safe fresh produce and protect health and environment. Quantitative comparisons highlighted the importance of selecting appropriate analytical methods based on the desired level of taxonomic delineation in each microbiome.