Variations in bacterial diversity and antibiotic resistance genes across diverse recycled and surface waters used for irrigation in the Mid-Atlantic and Southwest United States: A CONSERVE two-year field study

Authors: MALAYIL, LEENA - University Of Maryland; RAMACHANDRAN, PADMINI - University Of Maryland; CHATTOPADHYAY, SUHANA - University Of Maryland; ALLARD, SARA - University Of Maryland; BUI, ANTHONY - University Of Maryland; BUTRON, JICELL - University Of Maryland; CALLAHAN, MARY THERESA - University Of Maryland; CRADDOCK, HILLARY - University Of Maryland; MURRAY, RIANNA - University Of Maryland; East, Cheryl - Roberts; Sharma, Manan; KNIEL, KALMIA - University Of Delaware; MICALLEF, SHIRLEY - University Of Maryland; HASHEM, FAWZY - University Of Maryland Eastern Shore (UMES); GERBA, CHARLES - University Of Arizona; RAVISHANKAR, SADHANA - University Of Arizona; PARVEEN, SALINA - University Of Maryland Eastern Shore (UMES); MAY, ERIC - University Of Maryland Eastern Shore (UMES); HANDY, ERIC - US Department Of Agriculture (USDA); KULKARNI, PARACHI - University Of Maryland; ANDERSON-COUGHLIN, BRIENNA - University Of Delaware; CRAIGHEAD, SHANI - University Of Delaware; GARTLEY, SAMANTHA - University Of Delaware; VANORE, ADAM - University Of Delaware; DUNCAN, RICO - University Of Maryland Eastern Shore (UMES); FOUST, DEREK - University Of Maryland Eastern Shore (UMES); HAYMAKER, JOSEPH - University Of Maryland Eastern Shore (UMES); BETANCOURT, WALTER - University Of Arizona; ZHU, LIBIN - University Of Arizona; MONGODIN, EMANUEL - University Of Maryland; SAPKOTA, AMIR - University Of Maryland; SAPKOTA, AMY - University Of Maryland

Submitted to: Journal of Environmental Science and Technology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2022
Publication Date: 9/15/2022
Citation: Malayil, L., Ramachandran, P., Chattopadhyay, S., Allard, S.M., Bui, A., Butron, J., Callahan, M., Craddock, H., Murray, R., East, C.L., Sharma, M., Kniel, K.E., Micallef, S.A., Hashem, F., Gerba, C., Ravishankar, S., Parveen, S., May, E., Handy, E.T., Kulkarni, P., Anderson-Coughlin, B., Craighead, S., Gartley, S., Vanore, A., Duncan, R., Foust, D., Haymaker, J., Betancourt, W., Zhu, L., Mongodin, E., Sapkota, A., Sapkota, A.R. 2022. Variations in bacterial diversity and antibiotic resistance genes across diverse recycled and surface waters used for irrigation in the Mid-Atlantic and Southwest United States: A CONSERVE two-year field study. Journal of Environmental Science and Technology. https://doi.org/10.1021/acs.est.2c02281 .
DOI: https://doi.org/10.1021/acs.est.2c02281

Interpretive Summary: Irrigation water has received more attention lately as water avaibility and quality issues have been seen to affect agricultural crops grown in the U.S. Traditional water quality indicators based on the levels of fecal indicator bacteria like Escherichia coli and Enterococcus spp. are insufficient to capture emerging contaminants in irrigation waters antibiotic resistant genes, which can be spread to foodborne or enteric pathogens to make human infectiosn more severe. The current report assesses the microbial diversity of different water sources evaluated over 2 year time period in the Mid-Atlantic U.S. as part of the CONSERVE project. Over 400 water samples were collected over 24 months from different water types (river, pond, reclaimed waters). Seasonality and water source certainly affected the levels of microbial diversity observed in this study. Antibiotic resistance genes, heavy metal resistance genes, and biocide resistance genes were detected in these water sources as well, with levels varying based on seasonality. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins. These results will help farmers determine when their irrigation water sources may have higher levels of emerging contaminants, and aid them in designing appropriate mitigation strategies to safely irrigation fruit and vegetable crops to reduce transmission of bacteria carrying antimicrobial resistance genes.

Technical Abstract: The 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 both 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse irrigation water sources. We collected 1L water samples (n=410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, DNA-extracted, and PCR-amplified, and the 16S rRNA gene was sequenced using the Illumina HiSeq 2500. Metagenomic shotgun sequencing was also performed (n=110 samples) to characterize antibiotic, metal and biocide resistance genes. Bacterial alpha and beta diversity were significantly different (p<0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed in multiple sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. Our results suggest that some recycled and surface water sources may require additional treatment before being used to irrigate food crops.