Reduced availability
of agricultural water has spurred increased
interest in using recycled irrigation water for U.S. food crop production.
However, there are significant knowledge gaps concerning the microbiological
quality of these water sources. To address these gaps, we used 16S
rRNA gene and metagenomic sequencing to characterize taxonomic and
functional variations (e.g., antimicrobial resistance) in bacterial
communities across diverse recycled and surface water irrigation sources.
We collected 1 L water samples (n = 410) between
2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites)
U.S. Samples were filtered, and DNA was extracted. The V3–V4
regions of the 16S rRNA gene were then PCR amplified and sequenced.
Metagenomic sequencing was also performed to characterize antibiotic,
metal, and biocide resistance genes. Bacterial alpha and beta diversities
were significantly different (p < 0.001) across
water types and seasons. Pathogenic bacteria, such as Salmonella
enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types.
The most common antibiotic resistance genes identified coded against
macrolides/lincosamides/streptogramins, aminoglycosides, rifampin
and elfamycins, and their read counts fluctuated across seasons. We
also observed multi-metal and multi-biocide resistance across all
water types. To our knowledge, this is the most comprehensive longitudinal
study to date of U.S. recycled water and surface water used for irrigation.
Our findings improve understanding of the potential differences in
the risk of exposure to bacterial pathogens and antibiotic resistance
genes originating from diverse irrigation water sources across seasons
and U.S. regions.