Metagenome function reflects water quality properties throughout a model irrigation pond

Authors: RYAN, BLAUSTEIN - University Of Maryland; Smith, Jaclyn; MAGALY, TORO - University Of Maryland; Pachepsky, Yakov; Stocker, Matthew

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2025
Publication Date: 6/4/2025
Citation: Ryan, B., Smith, J.E., Magaly, T., Pachepsky, Y.A., Stocker, M.D. 2025. Metagenome function reflects water quality properties throughout a model irrigation pond. Frontiers in Microbiology. 16. Article e153596. https://doi.org/10.3389/fmicb.2025.1535096.
DOI: https://doi.org/10.3389/fmicb.2025.1535096

Interpretive Summary: Survival of pathogenic microorganisms in water sources depends on the properties of water as the microbial habitat. Physical and chemical properties are commonly used to characterize irrigation water properties. Much less, if anything, is known about the microbial communities as pathogen habitat components in irrigation water. Such information can be critical since microbial community structure is an influential factor in the survival of its members. We present the first attempt to characterize the microbial communities in irrigation water using metagenomics. In the studies of irrigation ponds, bacterial diversity, and community composition varied in depth but not with the time of day. Bacterial diversity, community composition, and metabolic gene profiles were significantly correlated with many water quality variables, such as turbidity, chlorophyll, and dissolved organic matter, indicating the potential for using predictive relationships when studying aquatic microbiomes. These results suggest the need and the feasibility of expanding the characterization of irrigation waters as microbial habitats. They will present interest to consultants and researchers involved in evaluating the microbial quality of irrigation waters.

Technical Abstract: The relationship between surface water microbiome function and water quality within agricultural systems has important implications for food safety. The present study explored intra-daily variation (i.e., 9:00, 12:00, 15:00) in metagenomes of a model irrigation pond at different sampling locations across the surface and in the water column (i.e., at 0, 1, 2 m depths). We characterized changes in water quality as related to microbiome taxonomic profiles, metabolic pathways, and antimicrobial resistance (AMR) and virulence genetic elements. At the surface, Microcystis aeruginosa and other members of Cyanobacteria, along with functional pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. Within the water column, diverse members of Proteobacteria and Actinobacteria emerged as more dominant, along with pathways related to respiration and amino acid biosynthesis. Various aspects of water quality, such as concentrations of chlorophyll, dissolved organic matter, ammonia, and food safety indicators (i.e., Escherichia coli), correlated with taxonomic and functional profiles of the water microbiome. Processing the metagenomes with de novo assembly further yielded metagenome-assembled genomes (MAGs) for 22 different strains, 12 of which appear to represent novel species. Nearly all strains encoded AMR, virulence, or other stress response traits. Nevertheless, water quality associations with specific AMR and virulence genetic elements were not consistently distinguished within the scope of this study. Overall, our findings highlight distinctions in water microbiome diversity at the surface and in the water column of irrigation ponds and demonstrate the ability to monitor the functional potential of key bacterial groups in agricultural environments with metagenomic surveillance.