Effects of sampling location, depth, and time of day as factors influencing the results of metagenomic surveys of irrigation pond water

Routine water quality assessments of irrigation resources are crucial for supporting food safety. Although microbial communities in agricultural waters associate with water properties, the connection between microbiome function water quality is not well understood. This study used shotgun metagenomics to explore intra-daily variation in microbiomes and their functions related to water quality (e.g., dissolved oxygen, nutrient dynamics, etc.) in a model agricultural pond. At the water surface, Microcystis aeruginosa and other members of Cyanobacteria, along with functional pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. Alternatively, within the water column at 1-2m depths, diverse members of Proteobacteria and Actinobacteria were dominant, along with functional pathways more specifically related to respiration and amino acid biosynthesis. Various aspects of water quality, such as E. coli levels, which increased with water depth, correlated with the taxonomic and functional diversity of the pond microbiomes (P<0.05 for each). Moreover, metagenome-assembled genomes (MAGs) were assembled for 22 unique strains (i.e., <99% ANI) representing prominent members of Cyanobacteria and Proteobacteria, among other phyla. Antimicrobial resistance genes and virulence factors were detected throughout the pond and linked to specific strains. Overall, our findings demonstrate distinctions in pond water metagenomes at the surface and deeper into the water column, which have implications for monitoring in water quality assessments of agricultural resources.

Presentation Preference: Poster

Primary Presenter: Matthew Stocker, USDA (matthew.stocker@usda.gov)

Authors:

Matthew Stocker, USDA Agricultural Research Service  (matthew.stocker@usda.gov)

Yakov Pachepsky, USDA Agricultural Research Service  (Yakov.Pachepsky@usda.gov)

Jackie Smith, USDA Agricultural Research Service  (Jackie.Smith@usda.gov)

Ryan Blaustein, University of Maryland Department of Food Science and Nutrition  (rblauste@umd.edu)